Sun May 19 22:52:33 UTC 2024 I: starting to build vg/unstable/amd64 on jenkins on '2024-05-19 22:52' Sun May 19 22:52:33 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/21255/console.log Sun May 19 22:52:33 UTC 2024 I: Downloading source for unstable/vg=1.30.0+ds-1 --2024-05-19 22:52:33-- http://deb.debian.org/debian/pool/main/v/vg/vg_1.30.0%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2979 (2.9K) [text/prs.lines.tag] Saving to: ‘vg_1.30.0+ds-1.dsc’ 0K .. 100% 345M=0s 2024-05-19 22:52:33 (345 MB/s) - ‘vg_1.30.0+ds-1.dsc’ saved [2979/2979] Sun May 19 22:52:33 UTC 2024 I: vg_1.30.0+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vg Binary: vg, vg-docs Architecture: amd64 arm64 ppc64el mips64el s390x riscv64 x32 all Version: 1.30.0+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/vgteam/vg#vg Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/vg Vcs-Git: https://salsa.debian.org/med-team/vg.git Testsuite: autopkgtest Testsuite-Triggers: libvcflib-tools Build-Depends: debhelper-compat (= 13), pv , bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa , protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools , unzip, librdf0-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils , rasqal-utils , bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack , tabix , xxd , libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools , libhts-dev, help2man , python3:any, libsimde-dev Build-Depends-Indep: doxygen , graphviz Package-List: vg deb science optional arch=amd64,arm64,ppc64el,mips64el,s390x,riscv64,x32 vg-docs deb doc optional arch=all Checksums-Sha1: 6d9ca5053fc709f7c3522b696bd1036358a7faeb 94998060 vg_1.30.0+ds.orig.tar.xz 2ddb9fd2b7d207014be459d138e023eaf5837b29 114272 vg_1.30.0+ds-1.debian.tar.xz Checksums-Sha256: 3a354af9f8a30fa53cf34e31963d82af39d4001bcf4599aac2c220b0316694d1 94998060 vg_1.30.0+ds.orig.tar.xz bf97b4a1ef47ae2b075ed84e370405a65f5b3f105155b2e110a59cc48c59eb11 114272 vg_1.30.0+ds-1.debian.tar.xz Files: c6a604a6b39953d8b0ca53bfe7c22833 94998060 vg_1.30.0+ds.orig.tar.xz 5ffa5e44326a7e187b0908fab7bafcf2 114272 vg_1.30.0+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmARVrgACgkQPCZ2P2xn 5uKZpQ//fbfMElS/MNHzud7lsVGljOQ8Rw1KFxXAlc8m2/QcgOvExuTunhXbM2Kn dw4u1lY48WbbJ6FuWbFV9XdPdmigLzq9wog2BAIvtQ1m8znXp5SS1kZBU1YbfOEb Otd7QQoDTFhnrzZErPgm8wJaLO+DOtQ/9sMeBLLjvilCZlD7x+eIQl6bss4MRWz1 0A5hUMpAg6j3y428ulBgPk25z0uj/xKxhMs+6j5Vz/yJeB7jjivlfLNJxJoCSUei o+tnd7iSzPnoM2dz8Q2z8GRff+QVbHSG1UGHJbp3OB5N0BVdpPMC7RWVxBw1V7Qj nJaYCechbaAmg03PxJ4PheBbi8LWmhxEDRz46W48oRvReqsQ5SEXDJ531liENH2i R4zjhsdr7bU2hvR8lwUx7cknlfM8IvbSsdHDNwof5KRpn26+G2HdJZqoKRzVjPPE meV2i8wAPq7XlD1JAWiY6U3cj38NJBNlc3DddrYZKo8OcNxYSWl7egaIibS7OI3J 0+8RLQ8TIv0duLyPHq1iRTIyLQX6ocr/vjAkwoKzQPyvIb3KoEtHrzayHKzPZv4U 6k4lZUIr9+Q2VWty7bqtLDbHuiizJVf5o652Mg5akICfhOvGBvpYbRuQ317jkZoM 6CTHDrT+VjOQ4f3j5X156PhyaUZ9tsIjjTAiE1uPgsuFICbmtPQ= =J0uw -----END PGP SIGNATURE----- Sun May 19 22:52:33 UTC 2024 I: Checking whether the package is not for us Sun May 19 22:52:33 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun May 19 22:52:33 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun May 19 23:26:38 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 19 10:52:37 -12 2024 I: pbuilder-time-stamp: 1716159157 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [vg_1.30.0+ds-1.dsc] I: copying [./vg_1.30.0+ds.orig.tar.xz] I: copying [./vg_1.30.0+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jan 27 12:04:08 2021 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./vg_1.30.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting vg in vg-1.30.0+ds dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-10 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 dpkg-source: info: applying fix-handlegraph I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1787231/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d272c8ed34d44006a090bd8d247b9894' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1787231' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TnbD1gcZ/pbuilderrc_D8AL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TnbD1gcZ/b1 --logfile b1/build.log vg_1.30.0+ds-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 19 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1787231/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, tabix, xxd, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, doxygen, graphviz dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19718 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on pv; however: Package pv is not installed. pbuilder-satisfydepends-dummy depends on bsdmainutils; however: Package bsdmainutils is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on rs; however: Package rs is not installed. pbuilder-satisfydepends-dummy depends on libffi-dev; however: Package libffi-dev is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on libprotoc-dev; however: Package libprotoc-dev is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on libjansson-dev; however: Package libjansson-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on libtool; however: Package libtool is not installed. pbuilder-satisfydepends-dummy depends on jq; however: Package jq is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on unzip; however: Package unzip is not installed. pbuilder-satisfydepends-dummy depends on librdf0-dev; however: Package librdf0-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on gtk-doc-tools; however: Package gtk-doc-tools is not installed. pbuilder-satisfydepends-dummy depends on raptor2-utils; however: Package raptor2-utils is not installed. pbuilder-satisfydepends-dummy depends on rasqal-utils; however: Package rasqal-utils is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on gawk; however: Package gawk is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libpixman-1-dev; however: Package libpixman-1-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libbackward-cpp-dev; however: Package libbackward-cpp-dev is not installed. pbuilder-satisfydepends-dummy depends on elfutils; however: Package elfutils is not installed. pbuilder-satisfydepends-dummy depends on libdw-dev; however: Package libdw-dev is not installed. pbuilder-satisfydepends-dummy depends on libelf-dev; however: Package libelf-dev is not installed. pbuilder-satisfydepends-dummy depends on libraptor2-dev; however: Package libraptor2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev; however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on fastahack; however: Package fastahack is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libtsl-hopscotch-map-dev; however: Package libtsl-hopscotch-map-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.1); however: Package libvcflib-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bison{a} bsdextrautils{a} bsdmainutils{a} bwa{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} docbook-xml{a} docbook-xsl{a} doxygen{a} dwz{a} elfutils{a} fastahack{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} gtk-doc-tools{a} help2man{a} icu-devtools{a} intltool-debian{a} jq{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libasm1t64{a} libavif16{a} libbackward-cpp-dev{a} libblas3{a} libblkid-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcdt5{a} libcgraph6{a} libclang-cpp16t64{a} libclang1-16t64{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdw-dev{a} libdw1t64{a} libedit2{a} libelf-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfmt9{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgmp-dev{a} libgmpxx4ldbl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libjansson-dev{a} libjbig0{a} libjemalloc-dev{a} libjemalloc2{a} libjpeg62-turbo{a} libjq1{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libllvm16t64{a} liblocale-gettext-perl{a} libltdl7{a} liblz4-dev{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmhash2{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libonig5{a} libosp5{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-util-perl{a} libpathplan4{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc-dev{a} libprotoc32t64{a} libpsl5t64{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraptor2-0{a} libraptor2-dev{a} librasqal3-dev{a} librasqal3t64{a} librav1e0{a} librdf0-dev{a} librdf0t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsigsegv2{a} libsimde-dev{a} libsm-dev{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libsparsehash-dev{a} libssh2-1t64{a} libssw-dev{a} libssw0{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsvtav1enc1d1{a} libsysprof-capture-4-dev{a} libtabixpp-dev{a} libtabixpp0t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtsl-hopscotch-map-dev{a} libuchardet0{a} libuv1t64{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib2{a} libwebp7{a} libwfa2-0{a} libwfa2-dev{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft2{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxslt1-dev{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libyajl-dev{a} libyajl2{a} libyuv0{a} libz3-4{a} libzstd-dev{a} littler{a} m4{a} man-db{a} media-types{a} ncal{a} netbase{a} opensp{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} pv{a} python3{a} python3-lxml{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3.11{a} python3.11-minimal{a} r-base{a} r-base-core{a} r-cran-boot{a} r-cran-class{a} r-cran-cli{a} r-cran-cluster{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-foreign{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-kernsmooth{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-nnet{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-rpart{a} r-cran-scales{a} r-cran-spatial{a} r-cran-survival{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} r-recommended{a} rapidjson-dev{a} raptor2-utils{a} rasqal-utils{a} readline-common{a} rs{a} samtools{a} sensible-utils{a} sgml-base{a} sgml-data{a} tabix{a} tzdata{a} ucf{a} unzip{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} xxd{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-liberation2 krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgpm2 libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib r-base-dev r-base-html r-cran-abind r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-pkgdown r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vdiffr r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html redland-utils shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 362 newly installed, 0 to remove and 0 not upgraded. Need to get 257 MB of archives. After unpacking 1036 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b2 [426 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.191-1 [22.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 21 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ncal amd64 12.1.8 [19.7 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 bsdmainutils all 12.1.8 [5952 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1+b1 [10.7 MB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libsub-prototype-perl amd64 0.03-2+b2 [9744 B] Get: 77 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 80 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-46 [73.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 docbook-xml all 4.5-13 [77.4 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libllvm16t64 amd64 1:16.0.6-27 [23.1 MB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libclang-cpp16t64 amd64 1:16.0.6-27 [11.5 MB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libclang1-16t64 amd64 1:16.0.6-27 [6581 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b1 [4913 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.191-1+b1 [246 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libasm1t64 amd64 0.191-1+b1 [28.5 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.191-1+b1 [28.5 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 elfutils amd64 0.191-1+b1 [492 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b1 [27.6 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 fastahack amd64 1.0.0+dfsg-11+b1 [12.6 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.2-9+b1 [39.8 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.2-9+b1 [63.6 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1888.20240509-4 [170 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.0.4-3 [106 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2 [157 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.2-9+b1 [42.2 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.2-9+b1 [682 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.2-9+b1 [189 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.2-9+b1 [198 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.2-9+b1 [614 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 xsltproc amd64 1.1.35-1+b1 [115 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 gtk-doc-tools all 1.34.0-1 [328 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libonig5 amd64 6.9.9-1 [189 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libjq1 amd64 1.7.1-3 [163 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 jq amd64 1.7.1-3 [77.6 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.1-1 [43.9 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.1-1 [200 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1+b1 [345 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-2.1+b1 [373 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 197 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b3 [314 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.0-3+b1 [129 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-2+b1 [54.8 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.0-3+b1 [58.9 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.2+dfsg-1+b4 [608 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1 [412 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.80.2-1 [1265 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.80.2-1 [123 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.80.2-1 [170 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.5-2+b1 [351 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.5-2+b2 [158 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.1-1 [25.9 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 46.0-1 [47.1 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.80.2-1 [136 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.80.2-1 [1741 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.42.2-1+b1 [573 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 226 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.0.10-1+b1 [64.8 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.3-1+b1 [36.1 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.4-1+b1 [5348 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-1 [181 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-1 [118 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-1 [107 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b1 [35.8 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.0-3+b1 [43.2 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-5 [538 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b1 [4860 B] Get: 242 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6 [18.8 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libelf-dev amd64 0.191-1+b1 [76.2 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libdw-dev amd64 0.191-1+b1 [325 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b1 [275 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libjansson-dev amd64 2.14-2+b2 [43.3 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-2+b1 [275 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-2+b1 [496 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 liblz4-dev amd64 1.9.4-2 [82.8 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libmhash2 amd64 0.9.9.9-9+b1 [92.4 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2 [349 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 268 http://deb.debian.org/debian unstable/main amd64 libprotobuf32t64 amd64 3.21.12-8.2 [963 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libprotobuf-lite32t64 amd64 3.21.12-8.2 [273 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libprotobuf-dev amd64 3.21.12-8.2 [1306 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libprotoc32t64 amd64 3.21.12-8.2 [864 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libprotoc-dev amd64 3.21.12-8.2 [972 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libyajl2 amd64 2.1.0-5+b1 [23.3 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libraptor2-0 amd64 2.0.16-3+b2 [176 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.3+b3 [787 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libxslt1-dev amd64 1.1.35-1+b1 [345 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libyajl-dev amd64 2.1.0-5+b1 [31.9 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libraptor2-dev amd64 2.0.16-3+b2 [210 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 librasqal3t64 amd64 0.9.33-2.1+b1 [191 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 librasqal3-dev amd64 0.9.33-2.1+b1 [229 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 librdf0t64 amd64 1.0.17-3.1+b1 [106 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 librdf0-dev amd64 1.0.17-3.1+b1 [237 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-14+b1 [24.0 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1 [10.1 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libtabixpp-dev amd64 1.1.2-2.1 [9652 B] Get: 291 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4 [60.5 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b1 [188 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libwfa2-dev amd64 2.3.3-4 [79.4 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libvcflib-dev amd64 1.0.9+dfsg1-3+b1 [77.9 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-13 [230 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.0-2 [28.2 MB] Get: 306 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-1 [16.0 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-60.2-1 [1111 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 r-cran-boot all 1.3-30-1 [622 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 r-cran-cluster amd64 2.1.6-1 [568 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 r-cran-foreign amd64 0.8.86-1 [250 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 r-cran-kernsmooth amd64 2.23-22-1 [90.9 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 r-cran-survival amd64 3.6-4-1 [6302 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 r-cran-spatial amd64 7.3-17-1 [128 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 r-recommended all 4.4.0-2 [2572 B] Get: 331 http://deb.debian.org/debian unstable/main amd64 r-base all 4.4.0-2 [14.3 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-0-2 [4127 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.1-2 [1405 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b1 [651 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 protobuf-compiler amd64 3.21.12-8.2 [84.4 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 pv amd64 1.8.5-2 [79.2 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 raptor2-utils amd64 2.0.16-3+b2 [34.9 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 rasqal-utils amd64 0.9.33-2.1+b1 [43.9 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 rs amd64 20200313-1 [15.5 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.19+ds-1.1+b1 [476 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 xxd amd64 2:9.1.0377-1 [94.8 kB] Fetched 257 MB in 10s (24.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19718 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b2_amd64.deb ... Unpacking flex (2.6.4-8.2+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libsigsegv2:amd64 (2.14-1+b1) ... Selecting previously unselected package gawk. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19943 files and directories currently installed.) Preparing to unpack .../0-gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package ucf. Preparing to unpack .../2-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../3-libdebuginfod-common_0.191-1_all.deb ... Unpacking libdebuginfod-common (0.191-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../4-liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../5-libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../7-python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20548 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21508 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.1-1_amd64.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../013-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package bc. Preparing to unpack .../019-bc_1.07.1-4_amd64.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package bison. Preparing to unpack .../020-bison_2%3a3.8.2+dfsg-1+b1_amd64.deb ... Unpacking bison (2:3.8.2+dfsg-1+b1) ... Selecting previously unselected package ncal. Preparing to unpack .../021-ncal_12.1.8_amd64.deb ... Unpacking ncal (12.1.8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../022-bsdmainutils_12.1.8_all.deb ... Unpacking bsdmainutils (12.1.8) ... Selecting previously unselected package bwa. Preparing to unpack .../023-bwa_0.7.17-7+b3_amd64.deb ... Unpacking bwa (0.7.17-7+b3) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../024-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../025-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../026-libarchive13t64_3.7.2-2_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.2-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../027-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../028-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../029-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../030-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../031-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../032-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../033-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../034-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../035-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../036-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../037-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../038-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../039-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../040-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../041-libcurl4t64_8.7.1-5_amd64.deb ... Unpacking libcurl4t64:amd64 (8.7.1-5) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../042-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../043-librhash0_1.4.3-3+b1_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../044-libuv1t64_1.48.0-4_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-4) ... 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:amd64 (46.0-1) ... Setting up libjemalloc-dev (5.3.0-2+b1) ... Setting up libbackward-cpp-dev (1.6-1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up zip (3.0-13) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libglib2.0-data (2.80.2-1) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up uuid-dev:amd64 (2.40.1-1) ... Setting up libpathplan4:amd64 (2.42.2-9+b1) ... Setting up libann0 (1.1.2+doc-9+b1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libtsl-hopscotch-map-dev (2.3.1-1) ... Setting up libasm1t64:amd64 (0.191-1+b1) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up bsdmainutils (12.1.8) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-4+b1) ... Setting up liblz4-dev:amd64 (1.9.4-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsepol-dev:amd64 (3.5-2+b1) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libdisorder-dev:amd64 (0.0.2+git20130809.8062ee1-4+b1) ... Setting up libltdl7:amd64 (2.4.7-7+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libfmt9:amd64 (9.1.0+ds1-2) ... Setting up libmhash2:amd64 (0.9.9.9-9+b1) ... Setting up libyajl-dev:amd64 (2.1.0-5+b1) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.4.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up pv (1.8.5-2) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up bison (2:3.8.2+dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libthai-data (0.1.29-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.29.3-1) ... Setting up libcdt5:amd64 (2.42.2-9+b1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libcgraph6:amd64 (2.42.2-9+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libprotoc32t64:amd64 (3.21.12-8.2) ... Setting up libde265-0:amd64 (1.0.15-1+b1) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.19+ds-1.1+b1) ... Setting up libyuv0:amd64 (0.0.1888.20240509-4) ... Setting up libssw0:amd64 (1.1-14+b1) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libjansson-dev:amd64 (2.14-2+b2) ... Setting up libonig5:amd64 (6.9.9-1) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b3) ... Setting up libdivsufsort-dev:amd64 (2.0.1-6) ... Setting up rs (20200313-1) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libblkid-dev:amd64 (2.40.1-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up flex (2.6.4-8.2+b2) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.5-2) ... Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libfml-dev:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libxau-dev:amd64 (1:1.0.9-1+b1) ... Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up protobuf-compiler (3.21.12-8.2) ... Setting up libice-dev:amd64 (2:1.0.10-1+b1) ... Setting up libssw-dev:amd64 (1.1-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libgirepository-2.0-0:amd64 (2.80.2-1) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up libselinux1-dev:amd64 (3.5-2+b2) ... Setting up libjq1:amd64 (1.7.1-3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libpng-dev:amd64 (1.6.43-5) ... Setting up libglib2.0-bin (2.80.2-1) ... Setting up fastahack (1.0.0+dfsg-11+b1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up opensp (1.5.2-15) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libllvm16t64:amd64 (1:16.0.6-27) ... Setting up libprotobuf-dev:amd64 (3.21.12-8.2) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libxdmcp-dev:amd64 (1:1.1.2-3+b1) ... Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libelf-dev:amd64 (0.191-1+b1) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up libsmithwaterman-dev:amd64 (0.0+git20160702.2610e25-12+b1) ... Setting up libgav1-1:amd64 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libgvpr2:amd64 (2.42.2-9+b1) ... Setting up libprotoc-dev:amd64 (3.21.12-8.2) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up jq (1.7.1-3) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libmount-dev:amd64 (2.40.1-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up python3.11 (3.11.9-1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libavif16:amd64 (1.0.4-3) ... Setting up libxcb1-dev:amd64 (1.17.0-1) ... Setting up libxslt1-dev:amd64 (1.1.35-1+b1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libdebuginfod-common (0.191-1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libsm-dev:amd64 (2:1.2.3-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up xsltproc (1.1.35-1+b1) ... Setting up libx11-dev:amd64 (2:1.8.7-1+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up python3 (3.11.8-1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up libclang1-16t64 (1:16.0.6-27) ... Setting up libcurl4-gnutls-dev:amd64 (8.7.1-5) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp16t64 (1:16.0.6-27) ... Setting up libdw-dev:amd64 (0.191-1+b1) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libfreetype-dev:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-shm0-dev:amd64 (1.17.0-1) ... Setting up doxygen (1.9.8+ds-2+b1) ... Setting up python3-packaging (24.0-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxcb-render0-dev:amd64 (1.17.0-1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up cmake (3.29.3-1+b1) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libsub-override-perl (0.11-1) ... Setting up libcairo-gobject2:amd64 (1.18.0-3+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libcairo-script-interpreter2:amd64 (1.18.0-3+b1) ... Setting up libglib2.0-dev-bin (2.80.2-1) ... Setting up libdebuginfod1t64:amd64 (0.191-1+b1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libfontconfig-dev:amd64 (2.15.0-1.1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libraptor2-0:amd64 (2.0.16-3+b2) ... Setting up raptor2-utils (2.0.16-3+b2) ... Setting up libhts-dev:amd64 (1.19+ds-1.1+b1) ... Setting up librasqal3t64:amd64 (0.9.33-2.1+b1) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up librdf0t64:amd64 (1.0.17-3.1+b1) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.80.2-1) ... Setting up r-base-core (4.4.0-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-farver (2.1.1-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up libraptor2-dev:amd64 (2.0.16-3+b2) ... Setting up libcairo2-dev:amd64 (1.18.0-3+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up rasqal-utils (0.9.33-2.1+b1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up elfutils (0.191-1+b1) ... Setting up r-cran-boot (1.3-30-1) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up r-cran-spatial (7.3-17-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-60.2-1) ... Setting up debhelper (13.15.3) ... Setting up librasqal3-dev (0.9.33-2.1+b1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-foreign (0.8.86-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up librdf0-dev (1.0.17-3.1+b1) ... Setting up r-cran-kernsmooth (2.23-22-1) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up libvcflib-dev:amd64 (1.0.9+dfsg1-3+b1) ... Setting up r-cran-class (7.3-22-2) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up libheif1:amd64 (1.17.6-1+b2) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b1) ... Setting up r-base (4.4.0-2) ... Setting up libgd3:amd64 (2.3.3-9+b3) ... Setting up libgvc6 (2.42.2-9+b1) ... Setting up r-cran-matrix (1.7-0-2) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ... Setting up graphviz (2.42.2-9+b1) ... Setting up r-cran-survival (3.6-4-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-recommended (4.4.0-2) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-7) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-13) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-46) ... Setting up gtk-doc-tools (1.34.0-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/vg-1.30.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../vg_1.30.0+ds-1_source.changes dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.30.0+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' find /build/reproducible-path/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j20 clean make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -rf ../bin ../lib cd cutest && make clean make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_clean: error: make -j20 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' dh_autoreconf --sourcedirectory=/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_configure debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' mkdir -p /build/reproducible-path/vg-1.30.0+ds/debian/help mkdir -p /build/reproducible-path/vg-1.30.0+ds/debian/vg/usr mkdir -p /build/reproducible-path/vg-1.30.0+ds/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make -j20 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /build/reproducible-path/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/reproducible-path/vg-1.30.0+ds/lib/ && cp obj/* /build/reproducible-path/vg-1.30.0+ds/obj && cp src/*.h /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.30.0+ds/include cp -r deps/sparsepp/sparsepp include/ rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/dynamic.hpp include/dynamic touch lib/cleaned_old_boost if [ ! -d obj ]; then mkdir -p obj; fi # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.30.0+ds/include/ . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.30.0+ds/include/ cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make cp ./deps/gfakluge/src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/ cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d lib ]; then mkdir -p lib; fi cp deps/sha1/*.h* /build/reproducible-path/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.30.0+ds/include cp -r deps/dozeu/simde include if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o CMake Warning (dev) at /usr/share/cmake-3.29/Modules/GNUInstallDirs.cmake:253 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" find bin obj lib -type f -delete if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Setting build type to 'Debug' as none was specified. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o rm -Rf include/google/protobuf deps/protobuf g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- The C compiler identification is GNU 13.2.0 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- The C compiler identification is GNU 13.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- The CXX compiler identification is GNU 13.2.0 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o diff: include/vg_environment_version.hpp: No such file or directory . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/reproducible-path/vg-1.30.0+ds/obj ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- The CXX compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ -- The C compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp ar rc cuTest.a *.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:7:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 6 | #include "haplotype_state_node.hpp" +++ |+#include 7 | #include ln -s `which shuf` bin/shuf ranlib cuTest.a . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/reproducible-path/vg-1.30.0+ds/lib/libvw.* /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:6, from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:1:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? +++ |+#include 1 | #ifndef HAPLOTYPE_STATE_TREE_H . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am make[3]: *** [makefile:79: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o] Error 1 make[3]: *** Waiting for unfinished jobs.... rm -f /build/reproducible-path/vg-1.30.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/reproducible-path/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:127:29: error: ‘SIZE_MAX’ was not declared in this scope 127 | size_t last_level_built = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:11:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 10 | #include +++ |+#include 11 | /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In constructor ‘optionIndex::optionIndex(char*, char*, const haplotypeCohort*, const std::vector*)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:15:42: error: ‘SIZE_MAX’ was not declared in this scope 15 | if((*ref_index_shared_indices)[i] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:3:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 2 | #include "set_of_extensions.hpp" +++ |+#include 3 | #include /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: error: ‘SIZE_MAX’ was not declared in this scope 56 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: error: ‘SIZE_MAX’ was not declared in this scope 64 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_position(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: error: ‘SIZE_MAX’ was not declared in this scope 130 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: error: ‘SIZE_MAX’ was not declared in this scope 179 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_read_only_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: error: ‘SIZE_MAX’ was not declared in this scope 187 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::final_ref_site() const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: error: ‘SIZE_MAX’ was not declared in this scope 229 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘void haplotypeManager::find_ref_only_sites_and_alleles()’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: error: ‘SIZE_MAX’ was not declared in this scope 349 | ref_index_shared_indices = vector(final_ref_site() + 1, SIZE_MAX); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::get_ref_index_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: error: ‘SIZE_MAX’ was not declared in this scope 366 | if(ref_index_shared_indices[i] == SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:61:1: error: control reaches end of non-void function [-Werror=return-type] 61 | } | ^ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:69:1: error: control reaches end of non-void function [-Werror=return-type] 69 | } | ^ . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info cc1plus: some warnings being treated as errors rm -f *.o g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp mv cuTest.a ../../lib/ . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/dozeu && cp deps/dozeu/*.h /build/reproducible-path/vg-1.30.0+ds/include/dozeu/ make[3]: *** [makefile:82: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o] Error 1 -- The CXX compiler identification is GNU 13.2.0 . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs -- Detecting CXX compiler ABI info . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/bin/c++ - skipped libhandlegraph is root project or external_project -- Detecting CXX compile features -- Configuring done (3.0s) -- Detecting CXX compile features - done Building in Debug mode -- Configuring done (3.0s) libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' -- Generating done (0.0s) -- Generating done (0.0s) gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC -B/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h mv ../lib/sonLib.h.tmp ../lib/sonLib.h make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend mv ../lib/jsmn.h.tmp ../lib/jsmn.h make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake "--color=" mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h make -f CMakeFiles/Makefile2 all mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' libtoolize: copying file 'acinclude.d/ltoptions.m4' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp g++ -Wl,-z,relro -Wl,-z,now -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h [ 14%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o [ 14%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/debug.cpp /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/rle_bwt.cpp [ 21%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp [ 28%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/cw-bwt.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [ 35%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o [ 42%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/benchmark.cpp /usr/bin/c++ -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp -- Detecting C compiler ABI info - done cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h [ 50%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -- Detecting CXX compiler ABI info - done mv 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CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o libtoolize: copying file 'acinclude.d/ltsugar.m4' /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cp inc/sonLibList.h ../lib/sonLibList.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h libtoolize: copying file 'acinclude.d/ltversion.m4' [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtoolize: copying file 'acinclude.d/lt~obsolete.m4' cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::serialize(std::ostream&) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:13:35: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 13 | uint32_t magic_number = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::deserialize(std::istream&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:41:25: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 41 | if (magic_number != get_magic_number()) { | ^~~~~~~~~~~~~~~~ | magic_number [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:163: CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:194:46: error: ‘uint32_t’ was not declared in this scope 194 | static constexpr int MAGIC_SIZE = sizeof(uint32_t) / sizeof(char); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:12:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 11 | #include +++ |+#include 12 | In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:7: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::serialized_data_resize(size_t)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:254:46: error: ‘get_magic_number’ was not declared in this scope 254 | *((uint32_t*)serializedData) = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void* handlegraph::TriviallySerializable::serialize_and_get_mapping(int) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:661:30: error: ‘get_magic_number’ was not declared in this scope 661 | magic_buffer = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::deserialize(int)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:898:31: error: ‘get_magic_number’ was not declared in this scope 898 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:953:31: error: ‘get_magic_number’ was not declared in this scope 953 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:191: CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o] Error 1 -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:440 ] Protobuf_USE_STATIC_LIBS = OFF cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -- Performing Test HAVE_CXA_DEMANGLE src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4958:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4958 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: *** [CMakeFiles/Makefile2:90: CMakeFiles/handlegraph_objs.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[2]: *** [Makefile:436: lib/libhandlegraph.a] Error 2 make[2]: *** Waiting for unfinished jobs.... -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:576 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:584 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:602 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.21.12 -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:616 ] /usr/bin/protoc reveals version 3.21.12 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.19 -- Checking for module 'jansson' -- Found jansson, version 2.14 -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Configuring done (5.3s) -- Generating done (0.0s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -Dcfgdir= -P /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 11%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append [ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 16%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o [ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -- Looking for C++ include cstdio - found /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 30%] Performing configure step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" -S /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build Re-run cmake no build system arguments CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at /usr/share/cmake-3.29/Modules/GNUInstallDirs.cmake:253 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot [ 57%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/debug.dir/debug.cpp.o -o debug -- Configuring done (9.5s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The C compiler identification is GNU 13.2.0 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 57%] Built target debug [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Generating done (1.3s) configure.ac:15: installing './compile' configure.ac:3: installing './missing' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cluster/Makefile.am: installing './depcomp' make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting C compiler ABI info - done make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build -- Detecting CXX compiler ABI info make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (3.9s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[2]: *** [Makefile:523: lib/libsublinearLS.a] Error 2 [ 42%] Performing build step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:129: CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[5]: *** [CMakeFiles/vgio_static.dir/build.make:101: CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o] Error 1 [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:85:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:93:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:56:58: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:64:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... make[5]: *** [CMakeFiles/vgio_static.dir/build.make:227: CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o] Error 1 [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend yes make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp checking for a race-free mkdir -p... make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes [ 66%] Linking CXX shared library libhandlegraph.so gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether make supports nested variables... ar rvs lib/libgssw.a obj/gssw.o /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o yes ar: creating lib/libgssw.a a - obj/gssw.o make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o [100%] Built target handlegraph_shared checking whether the C++ compiler works... /usr/bin/ranlib libhandlegraph.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build yes checking for C++ compiler default output file name... a.out In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:87:66: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:94:53: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:97:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:56:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:63:49: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:66:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ checking for suffix of executables... [ 47%] Performing install step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 [ 64%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs checking whether we are cross compiling... make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 64%] Built target benchmark no checking for suffix of object files... [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o Install the project... cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp /usr/bin/cmake -P cmake_install.cmake [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp o checking whether the compiler supports GNU C++... -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 50%] Completed 'handlegraph' yes checking whether g++ accepts -g... /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ^~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' yes checking for g++ option to enable C++11 features... [ 50%] Built target handlegraph make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 52%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc none needed checking whether make supports the include directive... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes (GNU style) checking dependency style of g++... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc3 checking how to run the C++ preprocessor... g++ -E In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp checking build system type... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [ 71%] Built target cw-bwt checking whether the compiler supports GNU C... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 78%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether gcc understands -c and -o together... [ 85%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' gcc3 checking for a sed that does not truncate output... [ 85%] Built target rle_bwt /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp /usr/bin/grep -E checking for fgrep... [ 57%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... [ 85%] Built target rle_lz77_v2 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... [ 59%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 92%] Linking CXX executable rle_lz77_v1 /usr/bin/dd bs=4096 count=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... make[5]: *** [CMakeFiles/vgio.dir/build.make:101: CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp yes checking for stdlib.h... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for string.h... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [ 92%] Built target rle_lz77_v1 [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp yes checking for inttypes.h... yes checking for stdint.h... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided yes checking for strings.h... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for sys/stat.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: *** [CMakeFiles/vgio.dir/build.make:129: CMakeFiles/vgio.dir/src/basic_stream.cpp.o] Error 1 yes checking for sys/types.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for unistd.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp yes checking for dlfcn.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [100%] Built target h0_lz77 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/* include/dynamic yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if g++ static flag -static works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if g++ supports -c -o file.o... g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking for boostlib >= 1.0 (100000)... ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:171: CMakeFiles/vgio_static.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... ranlib sonLib.a yes checking whether the Boost::Program_Options library is available... rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/ranlib libsdsl.a yes checking that generated files are newer than configure... done configure: creating ./config.status make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all config.status: creating Makefile make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 config.status: creating vowpalwabbit/config.h make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' config.status: executing depfiles commands Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp make[4]: *** [CMakeFiles/Makefile2:145: CMakeFiles/vgio.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp make[3]: *** [Makefile:139: all] Error 2 -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp make[2]: *** [Makefile:433: lib/libvgio.a] Error 2 -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.30.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking whether the Boost::Program_Options library is available... mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f vw active_interactor rm -f ./so_locations make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f spanning_tree rm -f ../vowpalwabbit/*.o make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f library_example ezexample_train ezexample_predict make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. 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$depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall 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parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include 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-fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_args.cc: In function ‘void parse_dictionary_argument(vw&, std::string)’: parse_args.cc:209:30: warning: pointer ‘ec’ used after ‘void free(void*)’ [-Wuse-after-free] 209 | VW::dealloc_example(all.p->lp.delete_label, *ec); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parse_args.cc:208:15: note: call to ‘void free(void*)’ here 208 | free(ec); | ~~~~^~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall 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-I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 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-isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: link: ranlib .libs/liballreduce.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/vw vw-main.o -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/reproducible-path/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit/ make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build: error: make -j20 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make -j20 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /build/reproducible-path/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/reproducible-path/vg-1.30.0+ds/lib/ && cp obj/* /build/reproducible-path/vg-1.30.0+ds/obj && cp src/*.h /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.30.0+ds/include/ rm -f lib/libboost_* make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f lib/cleaned_old_protobuf* Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' if [ ! -d bin ]; then mkdir -p bin; fi cd externalTools && make all if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d lib ]; then mkdir -p lib; fi rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' find bin obj lib -type f -delete cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_boost make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* rm -Rf include/google/protobuf deps/protobuf make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c CMake Warning (dev) at /usr/share/cmake-3.29/Modules/GNUInstallDirs.cmake:253 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/reproducible-path/vg-1.30.0+ds/obj if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi libhandlegraph is root project or external_project CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.0s) if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp -- Generating done (0.4s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- The CXX compiler identification is GNU 13.2.0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o mv cuTest.a ../../lib/ /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' -- The C compiler identification is GNU 13.2.0 [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ -- Detecting CXX compiler ABI info [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wl,-z,relro -Wl,-z,now -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Detecting CXX compiler ABI info - done gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/reproducible-path/vg-1.30.0+ds/lib/libvw.* /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit -- Detecting C compiler ABI info make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:7:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 6 | #include "haplotype_state_node.hpp" +++ |+#include 7 | #include mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h make[3]: *** [makefile:79: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o] Error 1 make[3]: *** Waiting for unfinished jobs.... cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cp inc/hashTableC.h ../lib/hashTableC.h.tmp [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:6, from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:1:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? +++ |+#include 1 | #ifndef HAPLOTYPE_STATE_TREE_H cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h rm -f /build/reproducible-path/vg-1.30.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/reproducible-path/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:127:29: error: ‘SIZE_MAX’ was not declared in this scope 127 | size_t last_level_built = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:11:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 10 | #include +++ |+#include 11 | mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In constructor ‘optionIndex::optionIndex(char*, char*, const haplotypeCohort*, const std::vector*)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:15:42: error: ‘SIZE_MAX’ was not declared in this scope 15 | if((*ref_index_shared_indices)[i] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:3:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 2 | #include "set_of_extensions.hpp" +++ |+#include 3 | #include /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: error: ‘SIZE_MAX’ was not declared in this scope 56 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: error: ‘SIZE_MAX’ was not declared in this scope 64 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? cp inc/sonLib.h ../lib/sonLib.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_position(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: error: ‘SIZE_MAX’ was not declared in this scope 130 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: error: ‘SIZE_MAX’ was not declared in this scope 179 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_read_only_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: error: ‘SIZE_MAX’ was not declared in this scope 187 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::final_ref_site() const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: error: ‘SIZE_MAX’ was not declared in this scope 229 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘void haplotypeManager::find_ref_only_sites_and_alleles()’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: error: ‘SIZE_MAX’ was not declared in this scope 349 | ref_index_shared_indices = vector(final_ref_site() + 1, SIZE_MAX); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::get_ref_index_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: error: ‘SIZE_MAX’ was not declared in this scope 366 | if(ref_index_shared_indices[i] == SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -- Detecting C compiler ABI info - done /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:61:1: error: control reaches end of non-void function [-Werror=return-type] 61 | } | ^ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:69:1: error: control reaches end of non-void function [-Werror=return-type] 69 | } | ^ cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h rm -f lib/libstructures.a cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp ar: creating lib/libstructures.a mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cc1plus: some warnings being treated as errors cp inc/sonLibList.h ../lib/sonLibList.h.tmp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' make[3]: *** [makefile:82: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o] Error 1 mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h ./autogen.sh: 22: [[: not found cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -- The CXX compiler identification is GNU 13.2.0 /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h -- Detecting CXX compiler ABI info cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:194:46: error: ‘uint32_t’ was not declared in this scope 194 | static constexpr int MAGIC_SIZE = sizeof(uint32_t) / sizeof(char); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:12:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 11 | #include +++ |+#include 12 | mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::serialize(std::ostream&) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:13:35: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 13 | uint32_t magic_number = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ cp inc/stSafeC.h ../lib/stSafeC.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::deserialize(std::istream&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:41:25: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 41 | if (magic_number != get_magic_number()) { | ^~~~~~~~~~~~~~~~ | magic_number [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:7: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::serialized_data_resize(size_t)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:254:46: error: ‘get_magic_number’ was not declared in this scope 254 | *((uint32_t*)serializedData) = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void* handlegraph::TriviallySerializable::serialize_and_get_mapping(int) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:661:30: error: ‘get_magic_number’ was not declared in this scope 661 | magic_buffer = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::deserialize(int)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:898:31: error: ‘get_magic_number’ was not declared in this scope 898 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:953:31: error: ‘get_magic_number’ was not declared in this scope 953 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:191: CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:163: CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o] Error 1 -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ libtoolize: copying file 'acinclude.d/ltsugar.m4' -- Performing Test HAVE_CXA_DEMANGLE libtoolize: copying file 'acinclude.d/ltversion.m4' src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtoolize: copying file 'acinclude.d/lt~obsolete.m4' -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:440 ] Protobuf_USE_STATIC_LIBS = OFF src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4958:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4958 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:576 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:584 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:602 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.21.12 -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:616 ] /usr/bin/protoc reveals version 3.21.12 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.19 -- Checking for module 'jansson' -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Found jansson, version 2.14 -- Configuring done (3.7s) -- Generating done (0.3s) make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: *** [CMakeFiles/Makefile2:90: CMakeFiles/handlegraph_objs.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[2]: *** [Makefile:436: lib/libhandlegraph.a] Error 2 make[2]: *** Waiting for unfinished jobs.... -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" -- Looking for C++ include cstdio - found make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -Dcfgdir= -P /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 11%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o [ 16%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 21%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp -- Configuring done (7.4s) [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 47%] Performing configure step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" -S /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C Re-run cmake no build system arguments CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 50%] Performing build step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' -- Generating done (0.9s) [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 [ 54%] Performing install step for 'handlegraph' [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[5]: *** [CMakeFiles/vgio_static.dir/build.make:227: CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Install configuration: "" -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 57%] Built target handlegraph [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: *** [CMakeFiles/vgio_static.dir/build.make:255: CMakeFiles/vgio_static.dir/src/stream.cpp.o] Error 1 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[2]: *** [Makefile:523: lib/libsublinearLS.a] Error 2 [ 59%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: *** [CMakeFiles/vgio_static.dir/build.make:129: CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o] Error 1 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:101: CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o] Error 1 impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ configure.ac:15: installing './compile' configure.ac:3: installing './missing' # Make dest directory cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:87:66: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:94:53: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:97:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:56:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:63:49: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:66:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cluster/Makefile.am: installing './depcomp' In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:85:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:93:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:56:58: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:64:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o [ 73%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp make[5]: *** [CMakeFiles/vgio.dir/build.make:129: CMakeFiles/vgio.dir/src/basic_stream.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ^~~~~ configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level make[5]: *** [CMakeFiles/vgio.dir/build.make:101: CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o] Error 1 [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o checking whether the C++ compiler works... cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for C++ compiler default output file name... a.out checking for suffix of executables... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp checking whether we are cross compiling... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking how to run the C++ preprocessor... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -E In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for gcc option to enable C11 features... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/types.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for unistd.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking dynamic linker characteristics... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:171: CMakeFiles/vgio_static.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes ranlib sonLib.a /usr/bin/ranlib libsdsl.a checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... rm *.o mv sonLib.a ../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:145: CMakeFiles/vgio.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm make[2]: *** [Makefile:433: lib/libvgio.a] Error 2 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' yes checking if g++ static flag -static works... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make -f CMakeFiles/Makefile2 all mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' yes checking if g++ supports -c -o file.o... Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: 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/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.30.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! yes checking for egrep... (cached) /usr/bin/grep -E checking for boostlib >= 1.0 (100000)... mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f vw active_interactor rm -f ./so_locations make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f spanning_tree rm -f ../vowpalwabbit/*.o make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f library_example ezexample_train ezexample_predict make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 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-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_args.cc: In function ‘void parse_dictionary_argument(vw&, std::string)’: parse_args.cc:209:30: warning: pointer ‘ec’ used after ‘void free(void*)’ [-Wuse-after-free] 209 | VW::dealloc_example(all.p->lp.delete_label, *ec); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parse_args.cc:208:15: note: call to ‘void free(void*)’ here 208 | free(ec); | ~~~~^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/vw vw-main.o -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/reproducible-path/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit/ make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build: error: make -j20 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make -j20 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /build/reproducible-path/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/reproducible-path/vg-1.30.0+ds/lib/ && cp obj/* /build/reproducible-path/vg-1.30.0+ds/obj && cp src/*.h /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' touch lib/cleaned_old_boost rm -Rf include/google/protobuf deps/protobuf rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* find bin obj lib -type f -delete gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/reproducible-path/vg-1.30.0+ds/obj g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi libhandlegraph is root project or external_projectif [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi make[2]: 'bin/shuf' is up to date. -- Configuring done (0.0s) if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/reproducible-path/vg-1.30.0+ds/lib/libvw.* /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp rm -f /build/reproducible-path/vg-1.30.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/reproducible-path/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am -- Generating done (0.3s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 -- The CXX compiler identification is GNU 13.2.0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o ar rc cuTest.a *.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- The CXX compiler identification is GNU 13.2.0 ranlib cuTest.a . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ -- Detecting CXX compiler ABI info make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o ./autogen.sh: 22: [[: not found -- The C compiler identification is GNU 13.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -- Detecting CXX compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wl,-z,relro -Wl,-z,now -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:7:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 6 | #include "haplotype_state_node.hpp" +++ |+#include 7 | #include make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:6, from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:1:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? +++ |+#include 1 | #ifndef HAPLOTYPE_STATE_TREE_H make[3]: *** [makefile:79: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o] Error 1 make[3]: *** Waiting for unfinished jobs.... libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:127:29: error: ‘SIZE_MAX’ was not declared in this scope 127 | size_t last_level_built = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:11:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 10 | #include +++ |+#include 11 | make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In constructor ‘optionIndex::optionIndex(char*, char*, const haplotypeCohort*, const std::vector*)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:15:42: error: ‘SIZE_MAX’ was not declared in this scope 15 | if((*ref_index_shared_indices)[i] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:3:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 2 | #include "set_of_extensions.hpp" +++ |+#include 3 | #include /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: error: ‘SIZE_MAX’ was not declared in this scope 56 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: error: ‘SIZE_MAX’ was not declared in this scope 64 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? mv ../lib/avl.h.tmp ../lib/avl.h /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_position(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: error: ‘SIZE_MAX’ was not declared in this scope 130 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: error: ‘SIZE_MAX’ was not declared in this scope 179 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_read_only_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: error: ‘SIZE_MAX’ was not declared in this scope 187 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::final_ref_site() const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: error: ‘SIZE_MAX’ was not declared in this scope 229 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘void haplotypeManager::find_ref_only_sites_and_alleles()’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: error: ‘SIZE_MAX’ was not declared in this scope 349 | ref_index_shared_indices = vector(final_ref_site() + 1, SIZE_MAX); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? cp inc/bioioC.h ../lib/bioioC.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::get_ref_index_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: error: ‘SIZE_MAX’ was not declared in this scope 366 | if(ref_index_shared_indices[i] == SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h -- Detecting C compiler ABI info - done [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o cp inc/jsmn.h ../lib/jsmn.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o mv ../lib/jsmn.h.tmp ../lib/jsmn.h /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp cp inc/sonLib.h ../lib/sonLib.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:61:1: error: control reaches end of non-void function [-Werror=return-type] 61 | } | ^ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:69:1: error: control reaches end of non-void function [-Werror=return-type] 69 | } | ^ mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp libtoolize: copying file 'acinclude.d/ltoptions.m4' mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ cc1plus: some warnings being treated as errors mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h make[3]: *** [makefile:82: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o] Error 1 cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h libtoolize: copying file 'acinclude.d/ltsugar.m4' cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp libtoolize: copying file 'acinclude.d/ltversion.m4' -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:440 ] Protobuf_USE_STATIC_LIBS = OFF [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o cp inc/sonLibString.h ../lib/sonLibString.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::serialize(std::ostream&) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:13:35: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 13 | uint32_t magic_number = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::deserialize(std::istream&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:41:25: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 41 | if (magic_number != get_magic_number()) { | ^~~~~~~~~~~~~~~~ | magic_number mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp inc/stJson.h ../lib/stJson.h.tmp make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:163: CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... mv ../lib/stJson.h.tmp ../lib/stJson.h rm -f lib/libstructures.a cp inc/stMatrix.h ../lib/stMatrix.h.tmp ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:576 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:584 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:602 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.21.12 -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:616 ] /usr/bin/protoc reveals version 3.21.12 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.19 In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:194:46: error: ‘uint32_t’ was not declared in this scope 194 | static constexpr int MAGIC_SIZE = sizeof(uint32_t) / sizeof(char); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:12:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 11 | #include +++ |+#include 12 | -- Checking for module 'jansson' In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:7: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::serialized_data_resize(size_t)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:254:46: error: ‘get_magic_number’ was not declared in this scope 254 | *((uint32_t*)serializedData) = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ -- Found jansson, version 2.14 /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void* handlegraph::TriviallySerializable::serialize_and_get_mapping(int) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:661:30: error: ‘get_magic_number’ was not declared in this scope 661 | magic_buffer = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::deserialize(int)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:898:31: error: ‘get_magic_number’ was not declared in this scope 898 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:953:31: error: ‘get_magic_number’ was not declared in this scope 953 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ -- Configuring done (3.4s) make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:191: CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o] Error 1 -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -Dcfgdir= -P /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 9%] No update step for 'handlegraph' [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o [ 16%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/cmake -E echo_append [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o [ 40%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 42%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: *** [CMakeFiles/Makefile2:90: CMakeFiles/handlegraph_objs.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[2]: *** [Makefile:436: lib/libhandlegraph.a] Error 2 make[2]: *** Waiting for unfinished jobs.... [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 47%] Performing configure step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" -S /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio Re-run cmake no build system arguments CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.0s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 52%] Performing build step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend -- Looking for C++ include cstdio - found make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4958:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4958 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot [ 54%] Performing install step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" -- Configuring done (6.2s) make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 57%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 57%] Built target handlegraph make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -- Generating done (0.7s) /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 59%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: *** [CMakeFiles/vgio_static.dir/build.make:227: CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 [ 66%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:129: CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o] Error 1 In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 73%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:255: CMakeFiles/vgio_static.dir/src/stream.cpp.o] Error 1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 76%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:101: CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o] Error 1 [ 78%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 80%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 85%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 88%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 92%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided configure.ac:15: installing './compile' configure.ac:3: installing './missing' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cluster/Makefile.am: installing './depcomp' make[5]: *** [CMakeFiles/vgio.dir/build.make:129: CMakeFiles/vgio.dir/src/basic_stream.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ make[5]: *** [CMakeFiles/vgio.dir/build.make:101: CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o] Error 1 /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: *** [CMakeFiles/vgio.dir/build.make:227: CMakeFiles/vgio.dir/src/message_iterator.cpp.o] Error 1 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[2]: *** [Makefile:523: lib/libsublinearLS.a] Error 2 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: *** [CMakeFiles/vgio.dir/build.make:255: CMakeFiles/vgio.dir/src/stream.cpp.o] Error 1 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ^~~~~ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:87:66: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:94:53: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:97:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:56:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:63:49: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:66:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:85:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:93:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:56:58: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:64:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o yes cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp yes checking whether make supports nested variables... yes In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp checking whether the C++ compiler works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for C++ compiler default output file name... a.out checking for suffix of executables... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether we are cross compiling... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ no checking for suffix of object files... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ o /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ checking whether the compiler supports GNU C++... /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether g++ accepts -g... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp yes checking for g++ option to enable C++11 features... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -E In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking build system type... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp checking whether the compiler supports GNU C... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp yes checking whether gcc accepts -g... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp yes checking for gcc option to enable C11 features... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking for a sed that does not truncate output... impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/stat.h... yes checking for sys/types.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:171: CMakeFiles/vgio_static.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for joinable pthread attribute... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a yes rm *.o checking that generated files are newer than configure... done configure: creating ./config.status mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:145: CMakeFiles/vgio.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[2]: *** [Makefile:433: lib/libvgio.a] Error 2 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... /usr/bin/ranlib libsdsl.a yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' checking for suffix of executables... [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks checking whether we are cross compiling... make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" no checking for suffix of object files... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' o checking whether the compiler supports GNU C++... [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall yes checking whether g++ accepts -g... make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake yes checking for g++ option to enable C++11 features... -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.30.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking whether the Boost::Program_Options library is available... mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f vw active_interactor rm -f ./so_locations make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f spanning_tree rm -f ../vowpalwabbit/*.o make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f library_example ezexample_train ezexample_predict make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 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-isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from global_data.h:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o parse_args.cc: In function ‘void parse_dictionary_argument(vw&, std::string)’: parse_args.cc:209:30: warning: pointer ‘ec’ used after ‘void free(void*)’ [-Wuse-after-free] 209 | VW::dealloc_example(all.p->lp.delete_label, *ec); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parse_args.cc:208:15: note: call to ‘void free(void*)’ here 208 | free(ec); | ~~~~^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest 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-Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand 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-I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/vw vw-main.o -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/reproducible-path/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit/ make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build: error: make -j20 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make -j20 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/reproducible-path/vg-1.30.0+ds/lib/ && cp obj/* /build/reproducible-path/vg-1.30.0+ds/obj && cp src/*.h /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c rm -Rf include/boost make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' touch lib/cleaned_old_boost cd quicktree_1.1 && make all CC="gcc -std=c99" rm -Rf include/google/protobuf deps/protobuf libhandlegraph is root project or external_project -- Configuring done (0.0s) make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi touch lib/cleaned_old_protobuf_v003 make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/reproducible-path/vg-1.30.0+ds/obj if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d lib ]; then mkdir -p lib; fi /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi make[2]: 'bin/shuf' is up to date. if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/reproducible-path/vg-1.30.0+ds/lib/libvw.* /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit make -f CMakeFiles/Makefile2 all g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tnode’: rm -f /build/reproducible-path/vg-1.30.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/reproducible-path/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- The CXX compiler identification is GNU 13.2.0 . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o ar rc cuTest.a *.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am ranlib cuTest.a -- The C compiler identification is GNU 13.2.0 rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs -- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 13.2.0 [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true -- Detecting CXX compiler ABI info ./autogen.sh: 22: [[: not found g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- Detecting C compiler ABI info - done g++ -Wl,-z,relro -Wl,-z,now -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:7:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 6 | #include "haplotype_state_node.hpp" +++ |+#include 7 | #include make[3]: *** [makefile:79: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp libtoolize: copying file 'acinclude.d/ltoptions.m4' [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:440 ] Protobuf_USE_STATIC_LIBS = OFF libtoolize: copying file 'acinclude.d/ltsugar.m4' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp libtoolize: copying file 'acinclude.d/ltversion.m4' mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:6, from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:1:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? +++ |+#include 1 | #ifndef HAPLOTYPE_STATE_TREE_H cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::serialize(std::ostream&) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:13:35: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 13 | uint32_t magic_number = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::deserialize(std::istream&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:41:25: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 41 | if (magic_number != get_magic_number()) { | ^~~~~~~~~~~~~~~~ | magic_number cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h libtoolize: copying file 'acinclude.d/lt~obsolete.m4' /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:127:29: error: ‘SIZE_MAX’ was not declared in this scope 127 | size_t last_level_built = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:11:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 10 | #include +++ |+#include 11 | cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In constructor ‘optionIndex::optionIndex(char*, char*, const haplotypeCohort*, const std::vector*)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:15:42: error: ‘SIZE_MAX’ was not declared in this scope 15 | if((*ref_index_shared_indices)[i] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:3:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 2 | #include "set_of_extensions.hpp" +++ |+#include 3 | #include make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:163: CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: error: ‘SIZE_MAX’ was not declared in this scope 56 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: error: ‘SIZE_MAX’ was not declared in this scope 64 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_position(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: error: ‘SIZE_MAX’ was not declared in this scope 130 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: error: ‘SIZE_MAX’ was not declared in this scope 179 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_read_only_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: error: ‘SIZE_MAX’ was not declared in this scope 187 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::final_ref_site() const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: error: ‘SIZE_MAX’ was not declared in this scope 229 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘void haplotypeManager::find_ref_only_sites_and_alleles()’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: error: ‘SIZE_MAX’ was not declared in this scope 349 | ref_index_shared_indices = vector(final_ref_site() + 1, SIZE_MAX); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::get_ref_index_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: error: ‘SIZE_MAX’ was not declared in this scope 366 | if(ref_index_shared_indices[i] == SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:576 ] requested version of Google Protobuf is cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:584 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:602 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.21.12 -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:616 ] /usr/bin/protoc reveals version 3.21.12 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -- Found htslib, version 1.19 mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:61:1: error: control reaches end of non-void function [-Werror=return-type] 61 | } | ^ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:69:1: error: control reaches end of non-void function [-Werror=return-type] 69 | } | ^ cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cc1plus: some warnings being treated as errors -- Checking for module 'jansson' cp inc/stGraph.h ../lib/stGraph.h.tmp cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h make[3]: *** [makefile:82: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o] Error 1 mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp -- Found jansson, version 2.14 -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp ar: creating lib/libstructures.a mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:194:46: error: ‘uint32_t’ was not declared in this scope 194 | static constexpr int MAGIC_SIZE = sizeof(uint32_t) / sizeof(char); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:12:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 11 | #include +++ |+#include 12 | -- Configuring done (4.7s) -- Generating done (0.1s) In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:7: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::serialized_data_resize(size_t)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:254:46: error: ‘get_magic_number’ was not declared in this scope 254 | *((uint32_t*)serializedData) = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void* handlegraph::TriviallySerializable::serialize_and_get_mapping(int) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:661:30: error: ‘get_magic_number’ was not declared in this scope 661 | magic_buffer = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::deserialize(int)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:898:31: error: ‘get_magic_number’ was not declared in this scope 898 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:953:31: error: ‘get_magic_number’ was not declared in this scope 953 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:191: CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o] Error 1 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' src/gssw.c: In function ‘gssw_sw_software_byte’: [ 2%] Creating directories for 'handlegraph' src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build /usr/bin/cmake -Dcfgdir= -P /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: *** [CMakeFiles/Makefile2:90: CMakeFiles/handlegraph_objs.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[2]: *** [Makefile:436: lib/libhandlegraph.a] Error 2 make[2]: *** Waiting for unfinished jobs.... [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append [ 7%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 11%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o [ 16%] No patch step for 'handlegraph' [ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/cmake -E echo_append [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 40%] Performing configure step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" -S /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp Re-run cmake no build system arguments CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 50%] Performing build step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -- Looking for C++ include cstdio - found make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Performing install step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp -- Configuring done (7.3s) /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 57%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' -- Generating done (0.9s) [ 57%] Built target handlegraph make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4958:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4958 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ [ 59%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided make[5]: *** [CMakeFiles/vgio_static.dir/build.make:227: CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 66%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:129: CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o] Error 1 In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o make[5]: *** [CMakeFiles/vgio_static.dir/build.make:255: CMakeFiles/vgio_static.dir/src/stream.cpp.o] Error 1 cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 76%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:101: CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o] Error 1 [ 78%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' [ 80%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 85%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:87:66: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:94:53: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:97:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:56:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:63:49: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:66:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 88%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:85:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:93:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:56:58: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:64:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ make[5]: *** [CMakeFiles/vgio.dir/build.make:101: CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ^~~~~ cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp make[5]: *** [CMakeFiles/vgio.dir/build.make:129: CMakeFiles/vgio.dir/src/basic_stream.cpp.o] Error 1 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[2]: *** [Makefile:523: lib/libsublinearLS.a] Error 2 /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes make[5]: *** [CMakeFiles/vgio.dir/build.make:227: CMakeFiles/vgio.dir/src/message_iterator.cpp.o] Error 1 [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o checking for a race-free mkdir -p... cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether the C++ compiler works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory yes checking for C++ compiler default output file name... a.out gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz checking for suffix of executables... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp checking whether we are cross compiling... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz no checking for suffix of object files... make[5]: *** [CMakeFiles/vgio.dir/build.make:255: CMakeFiles/vgio.dir/src/stream.cpp.o] Error 1 [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp o checking whether the compiler supports GNU C++... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ yes checking whether g++ accepts -g... /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for g++ option to enable C++11 features... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc3 checking how to run the C++ preprocessor... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' checking build system type... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ok In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o no checking for stdio.h... cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for stdlib.h... yes checking for string.h... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp yes checking for inttypes.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for stdint.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp yes checking for strings.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp yes checking for sys/stat.h... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/types.h... impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ yes checking for unistd.h... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ no checking dynamic linker characteristics... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[4]: *** [CMakeFiles/Makefile2:171: CMakeFiles/vgio_static.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:145: CMakeFiles/vgio.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[2]: *** [Makefile:433: lib/libvgio.a] Error 2 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E /usr/bin/ranlib libsdsl.a checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 yes checking for gcc option to enable C11 features... make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... make -f CMakeFiles/Makefile2 preinstall /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp BSD nm -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp checking whether ln -s works... yes checking the maximum length of command line arguments... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp 1572864 -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp checking for /usr/bin/ld option to reload object files... -r -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp checking for file... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp file checking for objdump... objdump checking how to recognize dependent libraries... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp pass_all -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp checking for dlltool... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp no -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp checking how to associate runtime and link libraries... printf %s\n -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp checking for ar... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp ar checking for archiver @FILE support... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.30.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f vw active_interactor rm -f ./so_locations make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f spanning_tree rm -f ../vowpalwabbit/*.o make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f library_example ezexample_train ezexample_predict make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 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/usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o parse_args.cc: In function ‘void parse_dictionary_argument(vw&, std::string)’: parse_args.cc:209:30: warning: pointer ‘ec’ used after ‘void free(void*)’ [-Wuse-after-free] 209 | VW::dealloc_example(all.p->lp.delete_label, *ec); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parse_args.cc:208:15: note: call to ‘void free(void*)’ here 208 | free(ec); | ~~~~^~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/vw vw-main.o -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/reproducible-path/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit/ make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build: error: make -j20 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make -j20 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/reproducible-path/vg-1.30.0+ds/lib/ && cp obj/* /build/reproducible-path/vg-1.30.0+ds/obj && cp src/*.h /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* rm -Rf include/boost touch lib/cleaned_old_boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi cd quicktree_1.1 && make all CC="gcc -std=c99" rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. touch lib/cleaned_old_protobuf_v003 if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' libhandlegraph is root project or external_project -- Configuring done (0.0s) gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/reproducible-path/vg-1.30.0+ds/obj g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d lib ]; then mkdir -p lib; fi make[2]: 'bin/shuf' is up to date. if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/reproducible-path/vg-1.30.0+ds/lib/libvw.* /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' g++ -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am rm -f /build/reproducible-path/vg-1.30.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/reproducible-path/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp -- The CXX compiler identification is GNU 13.2.0 . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am -- The C compiler identification is GNU 13.2.0 . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- Detecting CXX compiler ABI info . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true ar rc cuTest.a *.o -- The CXX compiler identification is GNU 13.2.0 ranlib cuTest.a ./autogen.sh: 22: [[: not found rm -f *.o -- Detecting CXX compiler ABI info mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done g++ -Wl,-z,relro -Wl,-z,now -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' -- Detecting C compiler ABI info - done [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o libtoolize: copying file 'acinclude.d/ltoptions.m4' /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::serialize(std::ostream&) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:13:35: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 13 | uint32_t magic_number = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp: In member function ‘virtual void handlegraph::Serializable::deserialize(std::istream&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp:41:25: error: ‘get_magic_number’ was not declared in this scope; did you mean ‘magic_number’? 41 | if (magic_number != get_magic_number()) { | ^~~~~~~~~~~~~~~~ | magic_number gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:163: CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o libtoolize: copying file 'acinclude.d/ltsugar.m4' In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:43:13: error: ‘uint32_t’ does not name a type 43 | virtual uint32_t get_magic_number() const = 0; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp:9:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 8 | #include +++ |+#include 9 | /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:194:46: error: ‘uint32_t’ was not declared in this scope 194 | static constexpr int MAGIC_SIZE = sizeof(uint32_t) / sizeof(char); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp:12:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’? 11 | #include +++ |+#include 12 | [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp In file included from /usr/include/arpa/inet.h:22, from /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:7: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::serialized_data_resize(size_t)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:254:46: error: ‘get_magic_number’ was not declared in this scope 254 | *((uint32_t*)serializedData) = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void* handlegraph::TriviallySerializable::serialize_and_get_mapping(int) const’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:661:30: error: ‘get_magic_number’ was not declared in this scope 661 | magic_buffer = htonl(get_magic_number()); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp: In member function ‘void handlegraph::TriviallySerializable::deserialize(int)’: /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:898:31: error: ‘get_magic_number’ was not declared in this scope 898 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp:953:31: error: ‘get_magic_number’ was not declared in this scope 953 | if (observed_magic != get_magic_number()) { | ^~~~~~~~~~~~~~~~ libtoolize: copying file 'acinclude.d/ltversion.m4' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") cp inc/avl.h ../lib/avl.h.tmp -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:440 ] Protobuf_USE_STATIC_LIBS = OFF mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp make[5]: *** [CMakeFiles/handlegraph_objs.dir/build.make:191: CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o] Error 1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.30.0+ds/include -L. -L/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success libtoolize: copying file 'acinclude.d/lt~obsolete.m4' mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:7:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 6 | #include "haplotype_state_node.hpp" +++ |+#include 7 | #include cp inc/hashTableC.h ../lib/hashTableC.h.tmp cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp make[3]: *** [makefile:79: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o] Error 1 make[3]: *** Waiting for unfinished jobs.... mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:576 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:584 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:602 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.21.12 cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp cp inc/sonLibList.h ../lib/sonLibList.h.tmp src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- [ /usr/share/cmake-3.29/Modules/FindProtobuf.cmake:616 ] /usr/bin/protoc reveals version 3.21.12 mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h -- Found htslib, version 1.19 cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:6, from /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:18:29: error: ‘SIZE_MAX’ was not declared in this scope 18 | size_t initial_position = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp:1:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? +++ |+#include 1 | #ifndef HAPLOTYPE_STATE_TREE_H cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp rm -f lib/libstructures.a cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o -- Checking for module 'jansson' -- Found jansson, version 2.14 /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:127:29: error: ‘SIZE_MAX’ was not declared in this scope 127 | size_t last_level_built = SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp:11:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 10 | #include +++ |+#include 11 | /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In constructor ‘optionIndex::optionIndex(char*, char*, const haplotypeCohort*, const std::vector*)’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:15:42: error: ‘SIZE_MAX’ was not declared in this scope 15 | if((*ref_index_shared_indices)[i] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:3:1: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? 2 | #include "set_of_extensions.hpp" +++ |+#include 3 | #include /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: error: ‘SIZE_MAX’ was not declared in this scope 56 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:56:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: error: ‘SIZE_MAX’ was not declared in this scope 64 | if((*ref_index_shared_indices)[ref_idx] != SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:64:46: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_position(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: error: ‘SIZE_MAX’ was not declared in this scope 130 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:130:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: error: ‘SIZE_MAX’ was not declared in this scope 179 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:179:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::read_index_to_read_only_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: error: ‘SIZE_MAX’ was not declared in this scope 187 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:187:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::final_ref_site() const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: error: ‘SIZE_MAX’ was not declared in this scope 229 | return SIZE_MAX; | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:229:12: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘void haplotypeManager::find_ref_only_sites_and_alleles()’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: error: ‘SIZE_MAX’ was not declared in this scope 349 | ref_index_shared_indices = vector(final_ref_site() + 1, SIZE_MAX); | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:349:69: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘std::size_t haplotypeManager::get_ref_index_shared_index(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: error: ‘SIZE_MAX’ was not declared in this scope 366 | if(ref_index_shared_indices[i] == SIZE_MAX) { | ^~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:366:37: note: ‘SIZE_MAX’ is defined in header ‘’; did you forget to ‘#include ’? cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp ar: creating lib/libstructures.a mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp -- Configuring done (4.9s) mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::more_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:61:1: error: control reaches end of non-void function [-Werror=return-type] 61 | } | ^ /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp: In member function ‘alleleValue optionIndex::less_likely(std::size_t) const’: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp:69:1: error: control reaches end of non-void function [-Werror=return-type] 69 | } | ^ mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h -- Generating done (0.2s) make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake cc1plus: some warnings being treated as errors cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[3]: *** [makefile:82: /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o] Error 1 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE [ 2%] Creating directories for 'handlegraph' src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -Dcfgdir= -P /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 11%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 16%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp -- Looking for C++ include cstdio [ 35%] Performing configure step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" -S /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp Re-run cmake no build system arguments CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.0s) impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 47%] Performing build step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4958:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4958 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build -- Looking for C++ include cstdio - found make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 50%] Performing install step for 'handlegraph' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[4]: *** [CMakeFiles/Makefile2:90: CMakeFiles/handlegraph_objs.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make[2]: *** [Makefile:436: lib/libhandlegraph.a] Error 2 make[2]: *** Waiting for unfinished jobs.... make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp -- Configuring done (8.4s) make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 57%] Built target handlegraph make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' cd /build/reproducible-path/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 59%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp -- Generating done (1.8s) /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided make[5]: *** [CMakeFiles/vgio_static.dir/build.make:227: CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [ 66%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:15: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided make[5]: *** [CMakeFiles/vgio_static.dir/build.make:255: CMakeFiles/vgio_static.dir/src/stream.cpp.o] Error 1 [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:129: CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o] Error 1 [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp make[5]: *** [CMakeFiles/vgio_static.dir/build.make:101: CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o] Error 1 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 76%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp configure.ac:15: installing './compile' configure.ac:3: installing './missing' In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:11: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp:19, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cluster/Makefile.am: installing './depcomp' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 78%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 80%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -fPIC -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[2]: *** [Makefile:523: lib/libsublinearLS.a] Error 2 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level make[5]: *** [CMakeFiles/vgio.dir/build.make:101: CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In static member function ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const std::string&)’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: *** [CMakeFiles/vgio.dir/build.make:129: CMakeFiles/vgio.dir/src/basic_stream.cpp.o] Error 1 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:85:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:93:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: at offset 8 into object ‘x’ of size 8 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:56:58: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_gamma::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:64:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp yes In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:87:66: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:94:53: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:97:60: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: at offset 8 into object ‘x’ of size 8 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’, inlined from ‘static uint64_t sdsl::bits::read_unary(const uint64_t*, uint8_t)’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:531:17, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:56:62: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:63:49: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In static member function ‘static uint64_t sdsl::bits::read_int(const uint64_t*, uint8_t, uint8_t)’, inlined from ‘sdsl::coder::elias_delta::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:66:56: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds=] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: at offset 8 into object ‘x’ of size 8 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether the C++ compiler works... /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: error: no matching function for call to ‘google::protobuf::io::CodedInputStream::SetTotalBytesLimit(long unsigned int, long unsigned int)’ 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int)’ 384 | void SetTotalBytesLimit(int total_bytes_limit); | ^~~~~~~~~~~~~~~~~~ /usr/include/google/protobuf/io/coded_stream.h:384:8: note: candidate expects 1 argument, 2 provided # Make dest directory [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... make[5]: *** [CMakeFiles/vgio.dir/build.make:227: CMakeFiles/vgio.dir/src/message_iterator.cpp.o] Error 1 gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp checking whether we are cross compiling... gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o no checking for suffix of object files... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp o checking whether the compiler supports GNU C++... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether g++ accepts -g... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes (GNU style) checking dependency style of g++... make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp gcc3 checking how to run the C++ preprocessor... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ^~~~~ g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking build system type... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking how to print strings... printf checking for gcc... gcc cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether the compiler supports GNU C... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ yes /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether gcc accepts -g... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for gcc option to enable C11 features... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp none needed checking whether gcc understands -c and -o together... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for stdlib.h... yes checking for string.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp yes checking for inttypes.h... yes checking for stdint.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for strings.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp yes checking for sys/stat.h... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp yes checking for sys/types.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for unistd.h... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc static flag -static works... In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking dynamic linker characteristics... impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking for boostlib >= 1.0 (100000)... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking whether the Boost::Program_Options library is available... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:171: CMakeFiles/vgio_static.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: *** [CMakeFiles/Makefile2:145: CMakeFiles/vgio.dir/all] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[3]: *** [Makefile:139: all] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[2]: *** [Makefile:433: lib/libvgio.a] Error 2 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" /usr/bin/ranlib libsdsl.a checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... make[6]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' yes [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 checking for a race-free mkdir -p... make[4]: Leaving directory 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Removing old files gawk checking whether make sets $(MAKE)... rm -rf '/build/reproducible-path/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 yes /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks checking whether make supports nested variables... make -f CMakeFiles/Makefile2 all yes make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 checking whether the C++ compiler works... make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/io.hpp yes -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap.hpp checking for C++ compiler default output file name... a.out -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp checking for suffix of executables... -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.30.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /usr/bin/grep -E checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 " LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f vw active_interactor rm -rf .libs _libs rm -f *.o rm -f *.lo rm -f ./so_locations make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -rf .libs _libs rm -f spanning_tree rm -f *.o rm -f *.lo rm -f ../vowpalwabbit/*.o make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -rf .libs _libs rm -f library_example ezexample_train ezexample_predict rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX 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-MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo 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-I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from global_data.h:8: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_args.cc: In function ‘void parse_dictionary_argument(vw&, std::string)’: parse_args.cc:209:30: warning: pointer ‘ec’ used after ‘void free(void*)’ [-Wuse-after-free] 209 | VW::dealloc_example(all.p->lp.delete_label, *ec); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parse_args.cc:208:15: note: call to ‘void free(void*)’ here 208 | free(ec); | ~~~~^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from memory.h:5, from v_array.h:21: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. 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-Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:80, from /usr/include/boost/function/function_base.hpp:33, from /usr/include/boost/function/detail/prologue.hpp:18, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16: /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/shared_ptr.h:175:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 175 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/reproducible-path/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -L/build/reproducible-path/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 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make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. 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/build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/reproducible-path/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/reproducible-path/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/reproducible-path/vg-1.30.0+ds/include/vowpalwabbit/ make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build: error: make -j20 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:40: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make: *** [debian/rules:22: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1787231 and its subdirectories Sun May 19 23:26:39 UTC 2024 W: No second build log, what happened?