I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 7 06:50:20 -12 2024 I: pbuilder-time-stamp: 1704653420 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.mMqW2q7Y/trustedkeys.kbx': General error 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: failed to verify signature on ./vg_1.30.0+ds-1.dsc 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/2531716/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8a21ef38e103478896d03ba5edff71c5' 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='2531716' 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.UJFZmsgj/pbuilderrc_HxDc --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UJFZmsgj/b1 --logfile b1/build.log vg_1.30.0+ds-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.104:3128' I: uname -a Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 64856 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 182496 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 93744 Apr 10 2022 gzip -rwxr-xr-x 1 root root 18440 Nov 7 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 157864 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jan 20 2022 more -rwsr-xr-x 1 root root 51360 Jan 20 2022 mount -rwxr-xr-x 1 root root 14496 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 7 09:23 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jan 20 2022 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jan 20 2022 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2531716/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: arm64 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 ... 17734 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} 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} libann0{a} libarchive-zip-perl{a} libarchive13{a} libasm1{a} libbackward-cpp-dev{a} libblas3{a} libblkid-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost1.74-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-cpp11{a} libclang1-11{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdw-dev{a} libdw1{a} libedit2{a} libelf-dev{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfreetype-dev{a} libfreetype6{a} libfreetype6-dev{a} libfribidi0{a} libgd3{a} libgfortran5{a} libglib2.0-0{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} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libice-dev{a} libice6{a} libicu-dev{a} libicu67{a} libjansson-dev{a} libjansson4{a} libjbig0{a} libjemalloc-dev{a} libjemalloc2{a} libjpeg62-turbo{a} libjq1{a} libjsoncpp24{a} liblab-gamut1{a} liblapack3{a} libldap-2.4-2{a} libllvm11{a} liblocale-gettext-perl{a} libltdl7{a} liblz4-dev{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmhash2{a} libmount-dev{a} libmpdec3{a} libncurses-dev{a} libncurses5-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} libpathplan4{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix2{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpng-dev{a} libpng16-16{a} libprocps8{a} libprotobuf-dev{a} libprotobuf-lite23{a} libprotobuf23{a} libprotoc-dev{a} libprotoc23{a} libpsl5{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libraptor2-0{a} libraptor2-dev{a} librasqal3{a} librasqal3-dev{a} librdf0{a} librdf0-dev{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol1-dev{a} libsigsegv2{a} libsimde-dev{a} libsm-dev{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libsparsehash-dev{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libtsl-hopscotch-map-dev{a} libuchardet0{a} libuv1{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib1{a} libwebp6{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} libxt6{a} libyajl-dev{a} libyajl2{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} ncal{a} opensp{a} openssl{a} pkg-config{a} po-debconf{a} procps{a} protobuf-compiler{a} pv{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-lxml{a} python3-minimal{a} python3-pkg-resources{a} python3-pygments{a} python3.9{a} python3.9-minimal{a} r-base-core{a} r-cran-assertthat{a} r-cran-brio{a} r-cran-callr{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-crayon{a} r-cran-desc{a} r-cran-diffobj{a} r-cran-digest{a} r-cran-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-jsonlite{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-pillar{a} r-cran-pkgbuild{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-pkgload{a} r-cran-plyr{a} r-cran-praise{a} r-cran-prettyunits{a} r-cran-processx{a} r-cran-ps{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rematch2{a} r-cran-rlang{a} r-cran-rprojroot{a} r-cran-rstudioapi{a} r-cran-scales{a} r-cran-testthat{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-waldo{a} r-cran-withr{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-dev{a} x11proto-xext-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-liberation libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgpm2 libgts-bin libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx psmisc publicsuffix python3-bs4 python3-html5lib r-base-dev r-cran-abind r-cran-bit64 r-cran-cliapp r-cran-codetools r-cran-curl r-cran-data.table r-cran-dbi r-cran-domc r-cran-dplyr r-cran-generics r-cran-hexbin r-cran-hms r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-mockery r-cran-mockr r-cran-quantreg r-cran-rmarkdown r-cran-rsqlite r-cran-sp r-cran-vdiffr r-cran-xml2 r-doc-html r-recommended redland-utils shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 341 newly installed, 0 to remove and 0 not upgraded. Need to get 204 MB of archives. After unpacking 821 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8+deb11u1 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 flex arm64 2.6.4-8 [431 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 gawk arm64 1:5.1.0-1 [570 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2+deb11u5 [84.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 sgml-base all 1.30 [15.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2+deb11u2 [93.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1w-0+deb11u1 [837 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3+deb11u1 [273 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3+deb11u1 [123 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3+deb11u1 [69.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 bc arm64 1.07.1-2+b2 [107 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 bison arm64 2:3.7.5+dfsg-1 [1084 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 ncal arm64 12.1.7+nmu3 [29.5 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 bsdmainutils all 12.1.7+nmu3 [16.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 bwa arm64 0.7.17-6+b1 [198 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7+deb11u4 [629 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+deb11u1 [320 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1+deb11u1 [69.4 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1+deb11u1 [105 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3+deb11u1 [222 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+deb11u9 [326 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2+deb11u1 [3673 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 docbook all 4.5-6 [129 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libosp5 arm64 1.5.2-13+b2 [884 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 opensp arm64 1.5.2-13+b2 [414 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 docbook-to-man arm64 1:2.0.0-45 [75.6 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 docbook-xml all 4.5-9 [84.4 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 docbook-xsl all 1.79.2+dfsg-1 [1237 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1+deb11u1 [106 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libz3-4 arm64 4.8.10-1 [6117 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libllvm11 arm64 1:11.0.1-2 [14.7 MB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libclang-cpp11 arm64 1:11.0.1-2 [7957 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libclang1-11 arm64 1:11.0.1-2 [4553 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 doxygen arm64 1.9.1-1 [3891 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libdw1 arm64 0.183-1 [219 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libasm1 arm64 0.183-1 [30.5 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 elfutils arm64 0.183-1 [421 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-2 [4284 B] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libfastahack0 arm64 1.0.0+dfsg-7 [23.7 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 fastahack arm64 1.0.0+dfsg-7 [11.7 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1+deb11u1 [393 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 fontconfig arm64 2.13.1-4.2 [416 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libann0 arm64 1.1.2+doc-7 [25.1 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libcdt5 arm64 2.42.2-5 [61.2 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 libcgraph6 arm64 2.42.2-5 [82.7 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1+deb11u2 [244 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1+deb11u4 [278 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.2-1+deb11u1 [749 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libxpm4 arm64 1:3.5.12-1.1~deb11u1 [47.2 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libgd3 arm64 2.3.0-2 [127 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libgts-0.7-5 arm64 0.7.6+darcs121130-4+b1 [143 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-0 arm64 0.40.0-1.1~deb11u1 [445 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 libltdl7 arm64 2.4.6-15 [390 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libfribidi0 arm64 1.0.8-2+deb11u1 [64.9 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libthai-data all 0.1.28-3 [170 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 libthai0 arm64 0.1.28-3 [53.0 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 libpango-1.0-0 arm64 1.46.2-3 [183 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [59.4 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [48.6 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 libpathplan4 arm64 2.42.2-5 [62.6 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 libgvc6 arm64 2.42.2-5 [632 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 libgvpr2 arm64 2.42.2-5 [201 kB] Get: 139 http://deb.debian.org/debian bullseye/main arm64 liblab-gamut1 arm64 2.42.2-5 [220 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 libxaw7 arm64 2:1.0.13-1.1 [184 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 graphviz arm64 2.42.2-5 [586 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 libxslt1.1 arm64 1.1.34-4+deb11u1 [229 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 python3-lxml arm64 4.6.3+dfsg-0.1+deb11u1 [991 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 xsltproc arm64 1.1.34-4+deb11u1 [124 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 gtk-doc-tools all 1.33.2-1 [329 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 icu-devtools arm64 67.1-7 [189 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 libonig5 arm64 6.9.6-1.1 [176 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 libjq1 arm64 1.6-2.1 [121 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 jq arm64 1.6-2.1 [64.5 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 libbackward-cpp-dev all 1.5-2 [31.7 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3+deb11u1 [100 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 uuid-dev arm64 2.36.1-8+deb11u1 [99.6 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 libblkid-dev arm64 2.36.1-8+deb11u1 [229 kB] Get: 163 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 164 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options1.74.0 arm64 1.74.0-9 [344 kB] Get: 165 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options1.74-dev arm64 1.74.0-9 [382 kB] Get: 166 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options-dev arm64 1.74.0.3 [4340 B] Get: 167 http://deb.debian.org/debian bullseye/main arm64 libbrotli-dev arm64 1.0.9-2+b2 [277 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 169 http://deb.debian.org/debian bullseye/main arm64 libcairo-gobject2 arm64 1.16.0-5 [125 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get: 171 http://deb.debian.org/debian bullseye/main arm64 libcairo-script-interpreter2 arm64 1.16.0-5 [160 kB] Get: 172 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2+deb11u5 [128 kB] Get: 173 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2+deb11u2 [189 kB] Get: 174 http://deb.debian.org/debian bullseye/main arm64 libpng-dev arm64 1.6.37-3 [294 kB] Get: 175 http://deb.debian.org/debian bullseye/main arm64 libfreetype-dev arm64 2.10.4+dfsg-1+deb11u1 [554 kB] Get: 176 http://deb.debian.org/debian bullseye/main arm64 libfreetype6-dev arm64 2.10.4+dfsg-1+deb11u1 [82.6 kB] Get: 177 http://deb.debian.org/debian bullseye/main arm64 libfontconfig-dev arm64 2.13.1-4.2 [367 kB] Get: 178 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1-dev arm64 2.13.1-4.2 [238 kB] Get: 179 http://deb.debian.org/debian bullseye/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 180 http://deb.debian.org/debian bullseye/main arm64 x11proto-dev all 2020.1-1 [594 kB] Get: 181 http://deb.debian.org/debian bullseye/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB] Get: 182 http://deb.debian.org/debian bullseye/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get: 183 http://deb.debian.org/debian bullseye/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 184 http://deb.debian.org/debian bullseye/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get: 185 http://deb.debian.org/debian bullseye/main arm64 libxcb1-dev arm64 1.14-3 [177 kB] Get: 186 http://deb.debian.org/debian bullseye/main arm64 libx11-dev arm64 2:1.7.2-1+deb11u1 [829 kB] Get: 187 http://deb.debian.org/debian bullseye/main arm64 libxrender-dev arm64 1:0.9.10-1 [38.8 kB] Get: 188 http://deb.debian.org/debian bullseye/main arm64 x11proto-xext-dev all 2020.1-1 [3404 B] Get: 189 http://deb.debian.org/debian bullseye/main arm64 libxext-dev arm64 2:1.3.3-1.1 [107 kB] Get: 190 http://deb.debian.org/debian bullseye/main arm64 libice-dev arm64 2:1.0.10-1 [66.0 kB] Get: 191 http://deb.debian.org/debian bullseye/main arm64 libsm-dev arm64 2:1.2.3-1 [37.4 kB] Get: 192 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-dev arm64 0.40.0-1.1~deb11u1 [463 kB] Get: 193 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0-dev arm64 1.14-3 [114 kB] Get: 194 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0-dev arm64 1.14-3 [103 kB] Get: 195 http://deb.debian.org/debian bullseye/main arm64 libffi-dev arm64 3.3-6 [53.2 kB] Get: 196 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-data all 2.66.8-1 [1164 kB] Get: 197 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-bin arm64 2.66.8-1 [137 kB] Get: 198 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 199 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 200 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-dev-bin arm64 2.66.8-1 [177 kB] Get: 201 http://deb.debian.org/debian bullseye/main arm64 libsepol1-dev arm64 3.1-1 [329 kB] Get: 202 http://deb.debian.org/debian bullseye/main arm64 libpcre2-16-0 arm64 10.36-2+deb11u1 [203 kB] Get: 203 http://deb.debian.org/debian bullseye/main arm64 libpcre2-32-0 arm64 10.36-2+deb11u1 [194 kB] Get: 204 http://deb.debian.org/debian bullseye/main arm64 libpcre2-posix2 arm64 10.36-2+deb11u1 [49.1 kB] Get: 205 http://deb.debian.org/debian bullseye/main arm64 libpcre2-dev arm64 10.36-2+deb11u1 [647 kB] Get: 206 http://deb.debian.org/debian bullseye/main arm64 libselinux1-dev arm64 3.1-3 [171 kB] Get: 207 http://deb.debian.org/debian bullseye/main arm64 libmount-dev arm64 2.36.1-8+deb11u1 [78.0 kB] Get: 208 http://deb.debian.org/debian bullseye/main arm64 libpcre16-3 arm64 2:8.39-13 [236 kB] Get: 209 http://deb.debian.org/debian bullseye/main arm64 libpcre32-3 arm64 2:8.39-13 [229 kB] Get: 210 http://deb.debian.org/debian bullseye/main arm64 libpcrecpp0v5 arm64 2:8.39-13 [151 kB] Get: 211 http://deb.debian.org/debian bullseye/main arm64 libpcre3-dev arm64 2:8.39-13 [579 kB] Get: 212 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-dev arm64 2.66.8-1 [1592 kB] Get: 213 http://deb.debian.org/debian bullseye/main arm64 libcairo2-dev arm64 1.16.0-5 [712 kB] Get: 214 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+deb11u9 [323 kB] Get: 215 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+deb11u9 [425 kB] Get: 216 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 217 http://deb.debian.org/debian bullseye/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-2 [4348 B] Get: 218 http://deb.debian.org/debian bullseye/main arm64 libdivsufsort3 arm64 2.0.1-5 [38.9 kB] Get: 219 http://deb.debian.org/debian bullseye/main arm64 libdivsufsort-dev arm64 2.0.1-5 [19.1 kB] Get: 220 http://deb.debian.org/debian bullseye/main arm64 libelf-dev arm64 0.183-1 [76.4 kB] Get: 221 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2.1~deb11u1 [227 kB] Get: 222 http://deb.debian.org/debian bullseye/main arm64 libdw-dev arm64 0.183-1 [297 kB] Get: 223 http://deb.debian.org/debian bullseye/main arm64 libfastahack-dev arm64 1.0.0+dfsg-7 [26.0 kB] Get: 224 http://deb.debian.org/debian bullseye/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 225 http://deb.debian.org/debian bullseye/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 226 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 227 http://deb.debian.org/debian bullseye/main arm64 libgmpxx4ldbl arm64 2:6.2.1+dfsg-1+deb11u1 [337 kB] Get: 228 http://deb.debian.org/debian bullseye/main arm64 libgmp-dev arm64 2:6.2.1+dfsg-1+deb11u1 [625 kB] Get: 229 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 230 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 231 http://deb.debian.org/debian bullseye/main arm64 libicu-dev arm64 67.1-7 [9468 kB] Get: 232 http://deb.debian.org/debian bullseye/main arm64 libjansson4 arm64 2.13.1-1.1 [39.4 kB] Get: 233 http://deb.debian.org/debian bullseye/main arm64 libjansson-dev arm64 2.13.1-1.1 [43.3 kB] Get: 234 http://deb.debian.org/debian bullseye/main arm64 libjemalloc2 arm64 5.2.1-3 [192 kB] Get: 235 http://deb.debian.org/debian bullseye/main arm64 libjemalloc-dev arm64 5.2.1-3 [323 kB] Get: 236 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3+deb11u1 [1538 kB] Get: 237 http://deb.debian.org/debian bullseye/main arm64 liblz4-dev arm64 1.9.3-2 [73.5 kB] Get: 238 http://deb.debian.org/debian bullseye/main arm64 libmhash2 arm64 0.9.9.9-9 [99.9 kB] Get: 239 http://deb.debian.org/debian bullseye/main arm64 libncurses-dev arm64 6.2+20201114-2+deb11u2 [336 kB] Get: 240 http://deb.debian.org/debian bullseye/main arm64 libncurses5-dev arm64 6.2+20201114-2+deb11u2 [948 B] Get: 241 http://deb.debian.org/debian bullseye/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB] Get: 242 http://deb.debian.org/debian bullseye/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB] Get: 243 http://deb.debian.org/debian bullseye/main arm64 libprotobuf23 arm64 3.12.4-1+deb11u1 [781 kB] Get: 244 http://deb.debian.org/debian bullseye/main arm64 libprotobuf-lite23 arm64 3.12.4-1+deb11u1 [218 kB] Get: 245 http://deb.debian.org/debian bullseye/main arm64 libprotobuf-dev arm64 3.12.4-1+deb11u1 [1164 kB] Get: 246 http://deb.debian.org/debian bullseye/main arm64 libprotoc23 arm64 3.12.4-1+deb11u1 [703 kB] Get: 247 http://deb.debian.org/debian bullseye/main arm64 libprotoc-dev arm64 3.12.4-1+deb11u1 [850 kB] Get: 248 http://deb.debian.org/debian bullseye/main arm64 libyajl2 arm64 2.1.0-3+deb11u2 [23.5 kB] Get: 249 http://deb.debian.org/debian bullseye/main arm64 libraptor2-0 arm64 2.0.14-1.2 [155 kB] Get: 250 http://deb.debian.org/debian bullseye/main arm64 libxml2-dev arm64 2.9.10+dfsg-6.7+deb11u4 [753 kB] Get: 251 http://deb.debian.org/debian bullseye/main arm64 libxslt1-dev arm64 1.1.34-4+deb11u1 [329 kB] Get: 252 http://deb.debian.org/debian bullseye/main arm64 libyajl-dev arm64 2.1.0-3+deb11u2 [32.1 kB] Get: 253 http://deb.debian.org/debian bullseye/main arm64 libraptor2-dev arm64 2.0.14-1.2 [203 kB] Get: 254 http://deb.debian.org/debian bullseye/main arm64 librasqal3 arm64 0.9.33-0.1 [179 kB] Get: 255 http://deb.debian.org/debian bullseye/main arm64 librasqal3-dev arm64 0.9.33-0.1 [224 kB] Get: 256 http://deb.debian.org/debian bullseye/main arm64 librdf0 arm64 1.0.17-1.1+b1 [103 kB] Get: 257 http://deb.debian.org/debian bullseye/main arm64 librdf0-dev arm64 1.0.17-1.1+b1 [243 kB] Get: 258 http://deb.debian.org/debian bullseye/main arm64 libsimde-dev all 0.7.2-4 [259 kB] Get: 259 http://deb.debian.org/debian bullseye/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-11 [32.8 kB] Get: 260 http://deb.debian.org/debian bullseye/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-11 [37.4 kB] Get: 261 http://deb.debian.org/debian bullseye/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 262 http://deb.debian.org/debian bullseye/main arm64 libssw0 arm64 1.1-13 [18.5 kB] Get: 263 http://deb.debian.org/debian bullseye/main arm64 libssw-dev arm64 1.1-13 [21.9 kB] Get: 264 http://deb.debian.org/debian bullseye/main arm64 libtabixpp0 arm64 1.1.0-4 [8788 B] Get: 265 http://deb.debian.org/debian bullseye/main arm64 libtabixpp-dev arm64 1.1.0-4 [8108 B] Get: 266 http://deb.debian.org/debian bullseye/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [964 kB] Get: 267 http://deb.debian.org/debian bullseye/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 268 http://deb.debian.org/debian bullseye/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 269 http://deb.debian.org/debian bullseye/main arm64 libtk8.6 arm64 8.6.11-2 [738 kB] Get: 270 http://deb.debian.org/debian bullseye/main arm64 libtsl-hopscotch-map-dev all 2.3.0-1 [36.4 kB] Get: 271 http://deb.debian.org/debian bullseye/main arm64 libvcflib1 arm64 1.0.2+dfsg-2 [133 kB] Get: 272 http://deb.debian.org/debian bullseye/main arm64 libvcflib-dev arm64 1.0.2+dfsg-2 [84.9 kB] Get: 273 http://deb.debian.org/debian bullseye/main arm64 zip arm64 3.0-12 [228 kB] Get: 274 http://deb.debian.org/debian bullseye/main arm64 unzip arm64 6.0-26+deb11u1 [165 kB] Get: 275 http://deb.debian.org/debian bullseye/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 276 http://deb.debian.org/debian bullseye/main arm64 r-base-core arm64 4.0.4-1 [24.9 MB] Get: 277 http://deb.debian.org/debian bullseye/main arm64 r-cran-littler arm64 0.3.12-1 [95.1 kB] Get: 278 http://deb.debian.org/debian bullseye/main arm64 littler all 0.3.12-1 [15.6 kB] Get: 279 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get: 280 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcpp arm64 1.0.6-1 [2020 kB] Get: 281 http://deb.debian.org/debian bullseye/main arm64 r-cran-plyr arm64 1.8.6-2 [828 kB] Get: 282 http://deb.debian.org/debian bullseye/main arm64 r-cran-digest arm64 0.6.27-1 [185 kB] Get: 283 http://deb.debian.org/debian bullseye/main arm64 r-cran-glue arm64 1.4.2-1 [138 kB] Get: 284 http://deb.debian.org/debian bullseye/main arm64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get: 285 http://deb.debian.org/debian bullseye/main arm64 r-cran-brio arm64 1.1.1-1 [31.0 kB] Get: 286 http://deb.debian.org/debian bullseye/main arm64 r-cran-ps arm64 1.5.0-1 [275 kB] Get: 287 http://deb.debian.org/debian bullseye/main arm64 r-cran-r6 all 2.5.0-1 [104 kB] Get: 288 http://deb.debian.org/debian bullseye/main arm64 r-cran-processx arm64 3.4.5-1 [294 kB] Get: 289 http://deb.debian.org/debian bullseye/main arm64 r-cran-callr all 3.5.1-1 [386 kB] Get: 290 http://deb.debian.org/debian bullseye/main arm64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get: 291 http://deb.debian.org/debian bullseye/main arm64 r-cran-cli all 2.3.0-1 [480 kB] Get: 292 http://deb.debian.org/debian bullseye/main arm64 r-cran-crayon all 1.4.0-1 [143 kB] Get: 293 http://deb.debian.org/debian bullseye/main arm64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get: 294 http://deb.debian.org/debian bullseye/main arm64 r-cran-desc all 1.2.0-3 [301 kB] Get: 295 http://deb.debian.org/debian bullseye/main arm64 r-cran-rlang arm64 0.4.10-1 [1177 kB] Get: 296 http://deb.debian.org/debian bullseye/main arm64 r-cran-ellipsis arm64 0.3.1-1 [31.7 kB] Get: 297 http://deb.debian.org/debian bullseye/main arm64 r-cran-evaluate all 0.14-2 [81.1 kB] Get: 298 http://deb.debian.org/debian bullseye/main arm64 r-cran-jsonlite arm64 1.7.2+dfsg-1 [445 kB] Get: 299 http://deb.debian.org/debian bullseye/main arm64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get: 300 http://deb.debian.org/debian bullseye/main arm64 r-cran-magrittr arm64 2.0.1-1 [198 kB] Get: 301 http://deb.debian.org/debian bullseye/main arm64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get: 302 http://deb.debian.org/debian bullseye/main arm64 r-cran-withr all 2.4.1-1 [210 kB] Get: 303 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get: 304 http://deb.debian.org/debian bullseye/main arm64 r-cran-rstudioapi all 0.13-1 [262 kB] Get: 305 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgload arm64 1.1.0-1 [168 kB] Get: 306 http://deb.debian.org/debian bullseye/main arm64 r-cran-praise all 1.0.0-4 [20.1 kB] Get: 307 http://deb.debian.org/debian bullseye/main arm64 r-cran-diffobj arm64 0.3.2-1 [1069 kB] Get: 308 http://deb.debian.org/debian bullseye/main arm64 r-cran-fansi arm64 0.4.2-1 [340 kB] Get: 309 http://deb.debian.org/debian bullseye/main arm64 r-cran-utf8 arm64 1.1.4-2 [131 kB] Get: 310 http://deb.debian.org/debian bullseye/main arm64 r-cran-vctrs arm64 0.3.6-1 [1094 kB] Get: 311 http://deb.debian.org/debian bullseye/main arm64 r-cran-pillar all 1.4.7-1 [227 kB] Get: 312 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 313 http://deb.debian.org/debian bullseye/main arm64 r-cran-tibble arm64 3.0.6+dfsg-1 [416 kB] Get: 314 http://deb.debian.org/debian bullseye/main arm64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get: 315 http://deb.debian.org/debian bullseye/main arm64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get: 316 http://deb.debian.org/debian bullseye/main arm64 r-cran-testthat arm64 3.0.1-1 [1439 kB] Get: 317 http://deb.debian.org/debian bullseye/main arm64 r-cran-isoband arm64 0.2.3-2 [2062 kB] Get: 318 http://deb.debian.org/debian bullseye/main arm64 r-cran-mass arm64 7.3-53.1-1 [1114 kB] Get: 319 http://deb.debian.org/debian bullseye/main arm64 r-cran-lattice arm64 0.20-41-1+b1 [1164 kB] Get: 320 http://deb.debian.org/debian bullseye/main arm64 r-cran-nlme arm64 3.1.152-1 [2238 kB] Get: 321 http://deb.debian.org/debian bullseye/main arm64 r-cran-matrix arm64 1.3-2-1 [3559 kB] Get: 322 http://deb.debian.org/debian bullseye/main arm64 r-cran-mgcv arm64 1.8-34-1 [2978 kB] Get: 323 http://deb.debian.org/debian bullseye/main arm64 r-cran-farver arm64 2.0.3-1+b1 [1380 kB] Get: 324 http://deb.debian.org/debian bullseye/main arm64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get: 325 http://deb.debian.org/debian bullseye/main arm64 r-cran-colorspace arm64 2.0-0+dfsg-1 [1683 kB] Get: 326 http://deb.debian.org/debian bullseye/main arm64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 327 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get: 328 http://deb.debian.org/debian bullseye/main arm64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get: 329 http://deb.debian.org/debian bullseye/main arm64 r-cran-scales all 1.1.1-1 [557 kB] Get: 330 http://deb.debian.org/debian bullseye/main arm64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get: 331 http://deb.debian.org/debian bullseye/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 332 http://deb.debian.org/debian bullseye/main arm64 libvcflib-tools arm64 1.0.2+dfsg-2 [657 kB] Get: 333 http://deb.debian.org/debian bullseye/main arm64 protobuf-compiler arm64 3.12.4-1+deb11u1 [75.0 kB] Get: 334 http://deb.debian.org/debian bullseye/main arm64 pv arm64 1.6.6-1 [51.3 kB] Get: 335 http://deb.debian.org/debian bullseye/main arm64 rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB] Get: 336 http://deb.debian.org/debian bullseye/main arm64 raptor2-utils arm64 2.0.14-1.2 [35.2 kB] Get: 337 http://deb.debian.org/debian bullseye/main arm64 rasqal-utils arm64 0.9.33-0.1 [44.3 kB] Get: 338 http://deb.debian.org/debian bullseye/main arm64 rs arm64 20200313-1 [15.6 kB] Get: 339 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 340 http://deb.debian.org/debian bullseye/main arm64 tabix arm64 1.11-4 [316 kB] Get: 341 http://deb.debian.org/debian bullseye/main arm64 xxd arm64 2:8.2.2434-3+deb11u1 [192 kB] Fetched 204 MB in 6s (32.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17734 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_arm64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../5-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../6-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package flex. Preparing to unpack .../7-flex_2.6.4-8_arm64.deb ... Unpacking flex (2.6.4-8) ... Selecting previously unselected package readline-common. Preparing to unpack .../8-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../9-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Setting up readline-common (8.1-1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libsigsegv2:arm64 (2.13-1) ... 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 ... 18498 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.1.0-1_arm64.deb ... Unpacking gawk (1:5.1.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.10-2+deb11u5_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 18982 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package tzdata. Preparing to unpack .../2-tzdata_2021a-1+deb11u10_all.deb ... Unpacking tzdata (2021a-1+deb11u10) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../3-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../4-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../5-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 21241 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../002-libncurses6_6.2+20201114-2+deb11u2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package libprocps8:arm64. Preparing to unpack .../003-libprocps8_2%3a3.3.17-5_arm64.deb ... Unpacking libprocps8:arm64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.17-5_arm64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_1.1.1w-0+deb11u1_arm64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../009-libmagic1_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../012-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bc. Preparing to unpack .../017-bc_1.07.1-2+b2_arm64.deb ... Unpacking bc (1.07.1-2+b2) ... Selecting previously unselected package bison. Preparing to unpack .../018-bison_2%3a3.7.5+dfsg-1_arm64.deb ... Unpacking bison (2:3.7.5+dfsg-1) ... Selecting previously unselected package ncal. Preparing to unpack .../019-ncal_12.1.7+nmu3_arm64.deb ... Unpacking ncal (12.1.7+nmu3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../020-bsdmainutils_12.1.7+nmu3_all.deb ... Unpacking bsdmainutils (12.1.7+nmu3) ... Selecting previously unselected package bwa. Preparing to unpack .../021-bwa_0.7.17-6+b1_arm64.deb ... Unpacking bwa (0.7.17-6+b1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../022-cmake-data_3.18.4-2+deb11u1_all.deb ... Unpacking cmake-data (3.18.4-2+deb11u1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../023-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../024-libxml2_2.9.10+dfsg-6.7+deb11u4_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../025-libarchive13_3.4.3-2+deb11u1_arm64.deb ... Unpacking libarchive13:arm64 (3.4.3-2+deb11u1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../026-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../027-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../028-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../029-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../030-libnghttp2-14_1.43.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.43.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../031-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../032-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../033-libssh2-1_1.9.0-2_arm64.deb ... Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../034-libcurl4_7.74.0-1.3+deb11u9_arm64.deb ... Unpacking libcurl4:arm64 (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libjsoncpp24:arm64. Preparing to unpack .../035-libjsoncpp24_1.9.4-4_arm64.deb ... Unpacking libjsoncpp24:arm64 (1.9.4-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../036-librhash0_1.4.1-2_arm64.deb ... Unpacking librhash0:arm64 (1.4.1-2) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../037-libuv1_1.40.0-2_arm64.deb ... Unpacking libuv1:arm64 (1.40.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../038-cmake_3.18.4-2+deb11u1_arm64.deb ... Unpacking cmake (3.18.4-2+deb11u1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../039-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../040-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../041-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../042-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../043-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../044-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../045-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../046-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../047-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../048-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../049-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../050-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../051-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package xml-core. Preparing to unpack .../052-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package sgml-data. Preparing to unpack .../053-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../054-docbook_4.5-6_all.deb ... Unpacking docbook (4.5-6) ... Selecting previously unselected package libosp5. Preparing to unpack .../055-libosp5_1.5.2-13+b2_arm64.deb ... Unpacking libosp5 (1.5.2-13+b2) ... Selecting previously unselected package opensp. Preparing to unpack .../056-opensp_1.5.2-13+b2_arm64.deb ... Unpacking opensp (1.5.2-13+b2) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../057-docbook-to-man_1%3a2.0.0-45_arm64.deb ... Unpacking docbook-to-man (1:2.0.0-45) ... Selecting previously unselected package docbook-xml. Preparing to unpack .../058-docbook-xml_4.5-9_all.deb ... Unpacking docbook-xml (4.5-9) ... Selecting previously unselected package docbook-xsl. Preparing to unpack .../059-docbook-xsl_1.79.2+dfsg-1_all.deb ... Unpacking docbook-xsl (1.79.2+dfsg-1) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../060-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../061-libbsd0_0.11.3-1+deb11u1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1+deb11u1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../062-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../063-libz3-4_4.8.10-1_arm64.deb ... Unpacking libz3-4:arm64 (4.8.10-1) ... Selecting previously unselected package libllvm11:arm64. Preparing to unpack .../064-libllvm11_1%3a11.0.1-2_arm64.deb ... Unpacking libllvm11:arm64 (1:11.0.1-2) ... Selecting previously unselected package libclang-cpp11. Preparing to unpack .../065-libclang-cpp11_1%3a11.0.1-2_arm64.deb ... Unpacking libclang-cpp11 (1:11.0.1-2) ... Selecting previously unselected package libclang1-11. Preparing to unpack .../066-libclang1-11_1%3a11.0.1-2_arm64.deb ... Unpacking libclang1-11 (1:11.0.1-2) ... Selecting previously unselected package doxygen. Preparing to unpack .../067-doxygen_1.9.1-1_arm64.deb ... Unpacking doxygen (1.9.1-1) ... Selecting previously unselected package libdw1:arm64. Preparing to unpack .../068-libdw1_0.183-1_arm64.deb ... Unpacking libdw1:arm64 (0.183-1) ... Selecting previously unselected package libasm1:arm64. Preparing to unpack .../069-libasm1_0.183-1_arm64.deb ... Unpacking libasm1:arm64 (0.183-1) ... Selecting previously unselected package elfutils. Preparing to unpack .../070-elfutils_0.183-1_arm64.deb ... Unpacking elfutils (0.183-1) ... Selecting previously unselected package libdisorder0:arm64. Preparing to unpack .../071-libdisorder0_0.0.2+git20130809.8062ee1-2_arm64.deb ... Unpacking libdisorder0:arm64 (0.0.2+git20130809.8062ee1-2) ... Selecting previously unselected package libfastahack0. Preparing to unpack .../072-libfastahack0_1.0.0+dfsg-7_arm64.deb ... Unpacking libfastahack0 (1.0.0+dfsg-7) ... Selecting previously unselected package fastahack. Preparing to unpack .../073-fastahack_1.0.0+dfsg-7_arm64.deb ... Unpacking fastahack (1.0.0+dfsg-7) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../074-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../075-libfreetype6_2.10.4+dfsg-1+deb11u1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../076-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../077-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../078-libfontconfig1_2.13.1-4.2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.13.1-4.2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../079-fontconfig_2.13.1-4.2_arm64.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libann0. Preparing to unpack .../080-libann0_1.1.2+doc-7_arm64.deb ... Unpacking libann0 (1.1.2+doc-7) ... Selecting previously unselected package libcdt5:arm64. Preparing to unpack .../081-libcdt5_2.42.2-5_arm64.deb ... Unpacking libcdt5:arm64 (2.42.2-5) ... Selecting previously unselected package libcgraph6:arm64. Preparing to unpack .../082-libcgraph6_2.42.2-5_arm64.deb ... Unpacking libcgraph6:arm64 (2.42.2-5) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../083-libjpeg62-turbo_1%3a2.0.6-4_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.0.6-4) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../084-libdeflate0_1.7-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../085-libjbig0_2.1-3.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:arm64. Preparing to unpack .../086-libwebp6_0.6.1-2.1+deb11u2_arm64.deb ... Unpacking libwebp6:arm64 (0.6.1-2.1+deb11u2) ... Selecting previously unselected package libtiff5:arm64. Preparing to unpack .../087-libtiff5_4.2.0-1+deb11u4_arm64.deb ... Unpacking libtiff5:arm64 (4.2.0-1+deb11u4) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../088-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../089-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../090-libxcb1_1.14-3_arm64.deb ... Unpacking libxcb1:arm64 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../091-libx11-data_2%3a1.7.2-1+deb11u1_all.deb ... Unpacking libx11-data (2:1.7.2-1+deb11u1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../092-libx11-6_2%3a1.7.2-1+deb11u1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.7.2-1+deb11u1) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../093-libxpm4_1%3a3.5.12-1.1~deb11u1_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.12-1.1~deb11u1) ... Selecting previously unselected package libgd3:arm64. Preparing to unpack .../094-libgd3_2.3.0-2_arm64.deb ... Unpacking libgd3:arm64 (2.3.0-2) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../095-libglib2.0-0_2.66.8-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.66.8-1) ... Selecting previously unselected package libgts-0.7-5:arm64. Preparing to unpack .../096-libgts-0.7-5_0.7.6+darcs121130-4+b1_arm64.deb ... Unpacking libgts-0.7-5:arm64 (0.7.6+darcs121130-4+b1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../097-libpixman-1-0_0.40.0-1.1~deb11u1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.40.0-1.1~deb11u1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../098-libxcb-render0_1.14-3_arm64.deb ... Unpacking libxcb-render0:arm64 (1.14-3) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../099-libxcb-shm0_1.14-3_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.14-3) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../100-libxext6_2%3a1.3.3-1.1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.3-1.1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../101-libxrender1_1%3a0.9.10-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../102-libcairo2_1.16.0-5_arm64.deb ... Unpacking libcairo2:arm64 (1.16.0-5) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../103-libltdl7_2.4.6-15_arm64.deb ... Unpacking libltdl7:arm64 (2.4.6-15) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../104-libfribidi0_1.0.8-2+deb11u1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.8-2+deb11u1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../105-libgraphite2-3_1.3.14-1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../106-libharfbuzz0b_2.7.4-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (2.7.4-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../107-libthai-data_0.1.28-3_all.deb ... Unpacking libthai-data (0.1.28-3) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../108-libdatrie1_0.2.13-1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../109-libthai0_0.1.28-3_arm64.deb ... Unpacking libthai0:arm64 (0.1.28-3) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../110-libpango-1.0-0_1.46.2-3_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.46.2-3) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../111-libpangoft2-1.0-0_1.46.2-3_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.46.2-3) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../112-libpangocairo-1.0-0_1.46.2-3_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.46.2-3) ... Selecting previously unselected package libpathplan4:arm64. Preparing to unpack .../113-libpathplan4_2.42.2-5_arm64.deb ... Unpacking libpathplan4:arm64 (2.42.2-5) ... Selecting previously unselected package libgvc6. Preparing to unpack .../114-libgvc6_2.42.2-5_arm64.deb ... Unpacking libgvc6 (2.42.2-5) ... Selecting previously unselected package libgvpr2:arm64. Preparing to unpack .../115-libgvpr2_2.42.2-5_arm64.deb ... Unpacking libgvpr2:arm64 (2.42.2-5) ... Selecting previously unselected package liblab-gamut1:arm64. Preparing to unpack .../116-liblab-gamut1_2.42.2-5_arm64.deb ... Unpacking liblab-gamut1:arm64 (2.42.2-5) ... Selecting previously unselected package x11-common. Preparing to unpack .../117-x11-common_1%3a7.7+22_all.deb ... Unpacking x11-common (1:7.7+22) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../118-libice6_2%3a1.0.10-1_arm64.deb ... Unpacking libice6:arm64 (2:1.0.10-1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../119-libsm6_2%3a1.2.3-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:arm64. Preparing to unpack .../120-libxt6_1%3a1.2.0-1_arm64.deb ... Unpacking libxt6:arm64 (1:1.2.0-1) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../121-libxmu6_2%3a1.1.2-2+b3_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.2-2+b3) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../122-libxaw7_2%3a1.0.13-1.1_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.13-1.1) ... Selecting previously unselected package graphviz. Preparing to unpack .../123-graphviz_2.42.2-5_arm64.deb ... Unpacking graphviz (2.42.2-5) ... Selecting previously unselected package pkg-config. Preparing to unpack .../124-pkg-config_0.29.2-1_arm64.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package libxslt1.1:arm64. Preparing to unpack .../125-libxslt1.1_1.1.34-4+deb11u1_arm64.deb ... Unpacking libxslt1.1:arm64 (1.1.34-4+deb11u1) ... Selecting previously unselected package python3-lxml:arm64. Preparing to unpack .../126-python3-lxml_4.6.3+dfsg-0.1+deb11u1_arm64.deb ... Unpacking python3-lxml:arm64 (4.6.3+dfsg-0.1+deb11u1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../127-python3-pkg-resources_52.0.0-4_all.deb ... Unpacking python3-pkg-resources (52.0.0-4) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../128-python3-pygments_2.7.1+dfsg-2.1_all.deb ... Unpacking python3-pygments (2.7.1+dfsg-2.1) ... Selecting previously unselected package xsltproc. Preparing to unpack .../129-xsltproc_1.1.34-4+deb11u1_arm64.deb ... Unpacking xsltproc (1.1.34-4+deb11u1) ... Selecting previously unselected package gtk-doc-tools. Preparing to unpack .../130-gtk-doc-tools_1.33.2-1_all.deb ... Unpacking gtk-doc-tools (1.33.2-1) ... Selecting previously unselected package help2man. Preparing to unpack .../131-help2man_1.48.1_arm64.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../132-icu-devtools_67.1-7_arm64.deb ... Unpacking icu-devtools (67.1-7) ... Selecting previously unselected package libonig5:arm64. Preparing to unpack .../133-libonig5_6.9.6-1.1_arm64.deb ... Unpacking libonig5:arm64 (6.9.6-1.1) ... Selecting previously unselected package libjq1:arm64. Preparing to unpack .../134-libjq1_1.6-2.1_arm64.deb ... Unpacking libjq1:arm64 (1.6-2.1) ... Selecting previously unselected package jq. Preparing to unpack .../135-jq_1.6-2.1_arm64.deb ... Unpacking jq (1.6-2.1) ... Selecting previously unselected package libbackward-cpp-dev. Preparing to unpack .../136-libbackward-cpp-dev_1.5-2_all.deb ... Unpacking libbackward-cpp-dev (1.5-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../137-libblas3_3.9.0-3+deb11u1_arm64.deb ... Unpacking libblas3:arm64 (3.9.0-3+deb11u1) ... Selecting previously unselected package uuid-dev:arm64. Preparing to unpack .../138-uuid-dev_2.36.1-8+deb11u1_arm64.deb ... Unpacking uuid-dev:arm64 (2.36.1-8+deb11u1) ... Selecting previously unselected package libblkid-dev:arm64. Preparing to unpack .../139-libblkid-dev_2.36.1-8+deb11u1_arm64.deb ... Unpacking libblkid-dev:arm64 (2.36.1-8+deb11u1) ... Selecting previously unselected package libboost1.74-dev:arm64. Preparing to unpack .../140-libboost1.74-dev_1.74.0-9_arm64.deb ... Unpacking libboost1.74-dev:arm64 (1.74.0-9) ... Selecting previously unselected package libboost-program-options1.74.0:arm64. Preparing to unpack .../141-libboost-program-options1.74.0_1.74.0-9_arm64.deb ... Unpacking libboost-program-options1.74.0:arm64 (1.74.0-9) ... Selecting previously unselected package libboost-program-options1.74-dev:arm64. Preparing to unpack .../142-libboost-program-options1.74-dev_1.74.0-9_arm64.deb ... Unpacking libboost-program-options1.74-dev:arm64 (1.74.0-9) ... Selecting previously unselected package libboost-program-options-dev:arm64. Preparing to unpack .../143-libboost-program-options-dev_1.74.0.3_arm64.deb ... Unpacking libboost-program-options-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../144-libbrotli-dev_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../145-libbz2-dev_1.0.8-4_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-4) ... Selecting previously unselected package libcairo-gobject2:arm64. Preparing to unpack .../146-libcairo-gobject2_1.16.0-5_arm64.deb ... Unpacking libcairo-gobject2:arm64 (1.16.0-5) ... Selecting previously unselected package liblzo2-2:arm64. Preparing to unpack .../147-liblzo2-2_2.10-2_arm64.deb ... Unpacking liblzo2-2:arm64 (2.10-2) ... Selecting previously unselected package libcairo-script-interpreter2:arm64. Preparing to unpack .../148-libcairo-script-interpreter2_1.16.0-5_arm64.deb ... Unpacking libcairo-script-interpreter2:arm64 (1.16.0-5) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../149-libexpat1-dev_2.2.10-2+deb11u5_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.2.10-2+deb11u5) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../150-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2+deb11u2) ... Selecting previously unselected package libpng-dev:arm64. Preparing to unpack .../151-libpng-dev_1.6.37-3_arm64.deb ... Unpacking libpng-dev:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype-dev:arm64. Preparing to unpack .../152-libfreetype-dev_2.10.4+dfsg-1+deb11u1_arm64.deb ... Unpacking libfreetype-dev:arm64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package libfreetype6-dev:arm64. Preparing to unpack .../153-libfreetype6-dev_2.10.4+dfsg-1+deb11u1_arm64.deb ... Unpacking libfreetype6-dev:arm64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package libfontconfig-dev:arm64. Preparing to unpack .../154-libfontconfig-dev_2.13.1-4.2_arm64.deb ... Unpacking libfontconfig-dev:arm64 (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1-dev:arm64. Preparing to unpack .../155-libfontconfig1-dev_2.13.1-4.2_arm64.deb ... Unpacking libfontconfig1-dev:arm64 (2.13.1-4.2) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../156-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../157-x11proto-dev_2020.1-1_all.deb ... Unpacking x11proto-dev (2020.1-1) ... Selecting previously unselected package libxau-dev:arm64. Preparing to unpack .../158-libxau-dev_1%3a1.0.9-1_arm64.deb ... Unpacking libxau-dev:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:arm64. Preparing to unpack .../159-libxdmcp-dev_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp-dev:arm64 (1:1.1.2-3) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../160-xtrans-dev_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... Selecting previously unselected package libpthread-stubs0-dev:arm64. Preparing to unpack .../161-libpthread-stubs0-dev_0.4-1_arm64.deb ... Unpacking libpthread-stubs0-dev:arm64 (0.4-1) ... Selecting previously unselected package libxcb1-dev:arm64. Preparing to unpack .../162-libxcb1-dev_1.14-3_arm64.deb ... Unpacking libxcb1-dev:arm64 (1.14-3) ... Selecting previously unselected package libx11-dev:arm64. Preparing to unpack .../163-libx11-dev_2%3a1.7.2-1+deb11u1_arm64.deb ... Unpacking libx11-dev:arm64 (2:1.7.2-1+deb11u1) ... Selecting previously unselected package libxrender-dev:arm64. Preparing to unpack .../164-libxrender-dev_1%3a0.9.10-1_arm64.deb ... Unpacking libxrender-dev:arm64 (1:0.9.10-1) ... Selecting previously unselected package x11proto-xext-dev. Preparing to unpack .../165-x11proto-xext-dev_2020.1-1_all.deb ... Unpacking x11proto-xext-dev (2020.1-1) ... Selecting previously unselected package libxext-dev:arm64. Preparing to unpack .../166-libxext-dev_2%3a1.3.3-1.1_arm64.deb ... Unpacking libxext-dev:arm64 (2:1.3.3-1.1) ... Selecting previously unselected package libice-dev:arm64. Preparing to unpack .../167-libice-dev_2%3a1.0.10-1_arm64.deb ... Unpacking libice-dev:arm64 (2:1.0.10-1) ... Selecting previously unselected package libsm-dev:arm64. Preparing to unpack .../168-libsm-dev_2%3a1.2.3-1_arm64.deb ... Unpacking libsm-dev:arm64 (2:1.2.3-1) ... Selecting previously unselected package libpixman-1-dev:arm64. Preparing to unpack .../169-libpixman-1-dev_0.40.0-1.1~deb11u1_arm64.deb ... Unpacking libpixman-1-dev:arm64 (0.40.0-1.1~deb11u1) ... Selecting previously unselected package libxcb-render0-dev:arm64. Preparing to unpack .../170-libxcb-render0-dev_1.14-3_arm64.deb ... Unpacking libxcb-render0-dev:arm64 (1.14-3) ... Selecting previously unselected package libxcb-shm0-dev:arm64. Preparing to unpack .../171-libxcb-shm0-dev_1.14-3_arm64.deb ... Unpacking libxcb-shm0-dev:arm64 (1.14-3) ... Selecting previously unselected package libffi-dev:arm64. Preparing to unpack .../172-libffi-dev_3.3-6_arm64.deb ... Unpacking libffi-dev:arm64 (3.3-6) ... Selecting previously unselected package libglib2.0-data. Preparing to unpack .../173-libglib2.0-data_2.66.8-1_all.deb ... Unpacking libglib2.0-data (2.66.8-1) ... Selecting previously unselected package libglib2.0-bin. Preparing to unpack .../174-libglib2.0-bin_2.66.8-1_arm64.deb ... Unpacking libglib2.0-bin (2.66.8-1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../175-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../176-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package libglib2.0-dev-bin. Preparing to unpack .../177-libglib2.0-dev-bin_2.66.8-1_arm64.deb ... Unpacking libglib2.0-dev-bin (2.66.8-1) ... Selecting previously unselected package libsepol1-dev:arm64. Preparing to unpack .../178-libsepol1-dev_3.1-1_arm64.deb ... Unpacking libsepol1-dev:arm64 (3.1-1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../179-libpcre2-16-0_10.36-2+deb11u1_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../180-libpcre2-32-0_10.36-2+deb11u1_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-posix2:arm64. Preparing to unpack .../181-libpcre2-posix2_10.36-2+deb11u1_arm64.deb ... Unpacking libpcre2-posix2:arm64 (10.36-2+deb11u1) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../182-libpcre2-dev_10.36-2+deb11u1_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.36-2+deb11u1) ... Selecting previously unselected package libselinux1-dev:arm64. Preparing to unpack .../183-libselinux1-dev_3.1-3_arm64.deb ... Unpacking libselinux1-dev:arm64 (3.1-3) ... Selecting previously unselected package libmount-dev:arm64. Preparing to unpack .../184-libmount-dev_2.36.1-8+deb11u1_arm64.deb ... Unpacking libmount-dev:arm64 (2.36.1-8+deb11u1) ... Selecting previously unselected package libpcre16-3:arm64. Preparing to unpack .../185-libpcre16-3_2%3a8.39-13_arm64.deb ... Unpacking libpcre16-3:arm64 (2:8.39-13) ... Selecting previously unselected package libpcre32-3:arm64. Preparing to unpack .../186-libpcre32-3_2%3a8.39-13_arm64.deb ... Unpacking libpcre32-3:arm64 (2:8.39-13) ... Selecting previously unselected package libpcrecpp0v5:arm64. Preparing to unpack .../187-libpcrecpp0v5_2%3a8.39-13_arm64.deb ... Unpacking libpcrecpp0v5:arm64 (2:8.39-13) ... Selecting previously unselected package libpcre3-dev:arm64. Preparing to unpack .../188-libpcre3-dev_2%3a8.39-13_arm64.deb ... Unpacking libpcre3-dev:arm64 (2:8.39-13) ... Selecting previously unselected package libglib2.0-dev:arm64. Preparing to unpack .../189-libglib2.0-dev_2.66.8-1_arm64.deb ... Unpacking libglib2.0-dev:arm64 (2.66.8-1) ... Selecting previously unselected package libcairo2-dev:arm64. Preparing to unpack .../190-libcairo2-dev_1.16.0-5_arm64.deb ... Unpacking libcairo2-dev:arm64 (1.16.0-5) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../191-libcurl3-gnutls_7.74.0-1.3+deb11u9_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../192-libcurl4-gnutls-dev_7.74.0-1.3+deb11u9_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../193-libdeflate-dev_1.7-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.7-1) ... Selecting previously unselected package libdisorder-dev:arm64. Preparing to unpack .../194-libdisorder-dev_0.0.2+git20130809.8062ee1-2_arm64.deb ... Unpacking libdisorder-dev:arm64 (0.0.2+git20130809.8062ee1-2) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../195-libdivsufsort3_2.0.1-5_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-5) ... Selecting previously unselected package libdivsufsort-dev:arm64. Preparing to unpack .../196-libdivsufsort-dev_2.0.1-5_arm64.deb ... Unpacking libdivsufsort-dev:arm64 (2.0.1-5) ... Selecting previously unselected package libelf-dev:arm64. Preparing to unpack .../197-libelf-dev_0.183-1_arm64.deb ... Unpacking libelf-dev:arm64 (0.183-1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../198-liblzma-dev_5.2.5-2.1~deb11u1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.2.5-2.1~deb11u1) ... Selecting previously unselected package libdw-dev:arm64. Preparing to unpack .../199-libdw-dev_0.183-1_arm64.deb ... Unpacking libdw-dev:arm64 (0.183-1) ... Selecting previously unselected package libfastahack-dev. Preparing to unpack .../200-libfastahack-dev_1.0.0+dfsg-7_arm64.deb ... Unpacking libfastahack-dev (1.0.0+dfsg-7) ... Selecting previously unselected package libfml0:arm64. Preparing to unpack .../201-libfml0_0.1+git20190320.b499514-1+b1_arm64.deb ... Unpacking libfml0:arm64 (0.1+git20190320.b499514-1+b1) ... Selecting previously unselected package libfml-dev:arm64. Preparing to unpack .../202-libfml-dev_0.1+git20190320.b499514-1+b1_arm64.deb ... Unpacking libfml-dev:arm64 (0.1+git20190320.b499514-1+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../203-libgfortran5_10.2.1-6_arm64.deb ... Unpacking libgfortran5:arm64 (10.2.1-6) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../204-libgmpxx4ldbl_2%3a6.2.1+dfsg-1+deb11u1_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.2.1+dfsg-1+deb11u1) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../205-libgmp-dev_2%3a6.2.1+dfsg-1+deb11u1_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.2.1+dfsg-1+deb11u1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../206-libhts3_1.11-4_arm64.deb ... Unpacking libhts3:arm64 (1.11-4) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../207-libhts-dev_1.11-4_arm64.deb ... Unpacking libhts-dev:arm64 (1.11-4) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../208-libicu-dev_67.1-7_arm64.deb ... Unpacking libicu-dev:arm64 (67.1-7) ... Selecting previously unselected package libjansson4:arm64. Preparing to unpack .../209-libjansson4_2.13.1-1.1_arm64.deb ... Unpacking libjansson4:arm64 (2.13.1-1.1) ... Selecting previously unselected package libjansson-dev:arm64. Preparing to unpack .../210-libjansson-dev_2.13.1-1.1_arm64.deb ... Unpacking libjansson-dev:arm64 (2.13.1-1.1) ... Selecting previously unselected package libjemalloc2:arm64. Preparing to unpack .../211-libjemalloc2_5.2.1-3_arm64.deb ... Unpacking libjemalloc2:arm64 (5.2.1-3) ... Selecting previously unselected package libjemalloc-dev. Preparing to unpack .../212-libjemalloc-dev_5.2.1-3_arm64.deb ... Unpacking libjemalloc-dev (5.2.1-3) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../213-liblapack3_3.9.0-3+deb11u1_arm64.deb ... Unpacking liblapack3:arm64 (3.9.0-3+deb11u1) ... Selecting previously unselected package liblz4-dev:arm64. Preparing to unpack .../214-liblz4-dev_1.9.3-2_arm64.deb ... Unpacking liblz4-dev:arm64 (1.9.3-2) ... Selecting previously unselected package libmhash2:arm64. Preparing to unpack .../215-libmhash2_0.9.9.9-9_arm64.deb ... Unpacking libmhash2:arm64 (0.9.9.9-9) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../216-libncurses-dev_6.2+20201114-2+deb11u2_arm64.deb ... Unpacking libncurses-dev:arm64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package libncurses5-dev:arm64. Preparing to unpack .../217-libncurses5-dev_6.2+20201114-2+deb11u2_arm64.deb ... Unpacking libncurses5-dev:arm64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package libpaper1:arm64. Preparing to unpack .../218-libpaper1_1.1.28+b1_arm64.deb ... Unpacking libpaper1:arm64 (1.1.28+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../219-libpaper-utils_1.1.28+b1_arm64.deb ... Unpacking libpaper-utils (1.1.28+b1) ... Selecting previously unselected package libprotobuf23:arm64. Preparing to unpack .../220-libprotobuf23_3.12.4-1+deb11u1_arm64.deb ... Unpacking libprotobuf23:arm64 (3.12.4-1+deb11u1) ... Selecting previously unselected package libprotobuf-lite23:arm64. Preparing to unpack .../221-libprotobuf-lite23_3.12.4-1+deb11u1_arm64.deb ... Unpacking libprotobuf-lite23:arm64 (3.12.4-1+deb11u1) ... Selecting previously unselected package libprotobuf-dev:arm64. Preparing to unpack .../222-libprotobuf-dev_3.12.4-1+deb11u1_arm64.deb ... Unpacking libprotobuf-dev:arm64 (3.12.4-1+deb11u1) ... Selecting previously unselected package libprotoc23:arm64. Preparing to unpack .../223-libprotoc23_3.12.4-1+deb11u1_arm64.deb ... Unpacking libprotoc23:arm64 (3.12.4-1+deb11u1) ... Selecting previously unselected package libprotoc-dev:arm64. Preparing to unpack .../224-libprotoc-dev_3.12.4-1+deb11u1_arm64.deb ... Unpacking libprotoc-dev:arm64 (3.12.4-1+deb11u1) ... Selecting previously unselected package libyajl2:arm64. Preparing to unpack .../225-libyajl2_2.1.0-3+deb11u2_arm64.deb ... Unpacking libyajl2:arm64 (2.1.0-3+deb11u2) ... Selecting previously unselected package libraptor2-0:arm64. Preparing to unpack .../226-libraptor2-0_2.0.14-1.2_arm64.deb ... Unpacking libraptor2-0:arm64 (2.0.14-1.2) ... Selecting previously unselected package libxml2-dev:arm64. Preparing to unpack .../227-libxml2-dev_2.9.10+dfsg-6.7+deb11u4_arm64.deb ... Unpacking libxml2-dev:arm64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libxslt1-dev:arm64. Preparing to unpack .../228-libxslt1-dev_1.1.34-4+deb11u1_arm64.deb ... Unpacking libxslt1-dev:arm64 (1.1.34-4+deb11u1) ... Selecting previously unselected package libyajl-dev:arm64. Preparing to unpack .../229-libyajl-dev_2.1.0-3+deb11u2_arm64.deb ... Unpacking libyajl-dev:arm64 (2.1.0-3+deb11u2) ... Selecting previously unselected package libraptor2-dev. Preparing to unpack .../230-libraptor2-dev_2.0.14-1.2_arm64.deb ... Unpacking libraptor2-dev (2.0.14-1.2) ... Selecting previously unselected package librasqal3:arm64. Preparing to unpack .../231-librasqal3_0.9.33-0.1_arm64.deb ... Unpacking librasqal3:arm64 (0.9.33-0.1) ... Selecting previously unselected package librasqal3-dev. Preparing to unpack .../232-librasqal3-dev_0.9.33-0.1_arm64.deb ... Unpacking librasqal3-dev (0.9.33-0.1) ... Selecting previously unselected package librdf0:arm64. Preparing to unpack .../233-librdf0_1.0.17-1.1+b1_arm64.deb ... Unpacking librdf0:arm64 (1.0.17-1.1+b1) ... Selecting previously unselected package librdf0-dev. Preparing to unpack .../234-librdf0-dev_1.0.17-1.1+b1_arm64.deb ... Unpacking librdf0-dev (1.0.17-1.1+b1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../235-libsimde-dev_0.7.2-4_all.deb ... Unpacking libsimde-dev (0.7.2-4) ... Selecting previously unselected package libsmithwaterman0. Preparing to unpack .../236-libsmithwaterman0_0.0+git20160702.2610e25-11_arm64.deb ... Unpacking libsmithwaterman0 (0.0+git20160702.2610e25-11) ... Selecting previously unselected package libsmithwaterman-dev. Preparing to unpack .../237-libsmithwaterman-dev_0.0+git20160702.2610e25-11_arm64.deb ... Unpacking libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../238-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package libssw0:arm64. Preparing to unpack .../239-libssw0_1.1-13_arm64.deb ... Unpacking libssw0:arm64 (1.1-13) ... Selecting previously unselected package libssw-dev:arm64. Preparing to unpack .../240-libssw-dev_1.1-13_arm64.deb ... Unpacking libssw-dev:arm64 (1.1-13) ... Selecting previously unselected package libtabixpp0:arm64. Preparing to unpack .../241-libtabixpp0_1.1.0-4_arm64.deb ... Unpacking libtabixpp0:arm64 (1.1.0-4) ... Selecting previously unselected package libtabixpp-dev:arm64. Preparing to unpack .../242-libtabixpp-dev_1.1.0-4_arm64.deb ... Unpacking libtabixpp-dev:arm64 (1.1.0-4) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../243-libtcl8.6_8.6.11+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.11+dfsg-1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../244-libxft2_2.3.2-2_arm64.deb ... Unpacking libxft2:arm64 (2.3.2-2) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../245-libxss1_1%3a1.2.3-1_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../246-libtk8.6_8.6.11-2_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.11-2) ... Selecting previously unselected package libtsl-hopscotch-map-dev. Preparing to unpack .../247-libtsl-hopscotch-map-dev_2.3.0-1_all.deb ... Unpacking libtsl-hopscotch-map-dev (2.3.0-1) ... Selecting previously unselected package libvcflib1:arm64. Preparing to unpack .../248-libvcflib1_1.0.2+dfsg-2_arm64.deb ... Unpacking libvcflib1:arm64 (1.0.2+dfsg-2) ... Selecting previously unselected package libvcflib-dev:arm64. Preparing to unpack .../249-libvcflib-dev_1.0.2+dfsg-2_arm64.deb ... Unpacking libvcflib-dev:arm64 (1.0.2+dfsg-2) ... Selecting previously unselected package zip. Preparing to unpack .../250-zip_3.0-12_arm64.deb ... Unpacking zip (3.0-12) ... Selecting previously unselected package unzip. Preparing to unpack .../251-unzip_6.0-26+deb11u1_arm64.deb ... Unpacking unzip (6.0-26+deb11u1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../252-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../253-r-base-core_4.0.4-1_arm64.deb ... Unpacking r-base-core (4.0.4-1) ... Selecting previously unselected package r-cran-littler. Preparing to unpack .../254-r-cran-littler_0.3.12-1_arm64.deb ... Unpacking r-cran-littler (0.3.12-1) ... Selecting previously unselected package littler. Preparing to unpack .../255-littler_0.3.12-1_all.deb ... Unpacking littler (0.3.12-1) ... Selecting previously unselected package r-cran-pkgkitten. Preparing to unpack .../256-r-cran-pkgkitten_0.2.1-1_all.deb ... Unpacking r-cran-pkgkitten (0.2.1-1) ... Selecting previously unselected package r-cran-rcpp. Preparing to unpack .../257-r-cran-rcpp_1.0.6-1_arm64.deb ... Unpacking r-cran-rcpp (1.0.6-1) ... Selecting previously unselected package r-cran-plyr. Preparing to unpack .../258-r-cran-plyr_1.8.6-2_arm64.deb ... Unpacking r-cran-plyr (1.8.6-2) ... Selecting previously unselected package r-cran-digest. Preparing to unpack .../259-r-cran-digest_0.6.27-1_arm64.deb ... Unpacking r-cran-digest (0.6.27-1) ... Selecting previously unselected package r-cran-glue. Preparing to unpack .../260-r-cran-glue_1.4.2-1_arm64.deb ... Unpacking r-cran-glue (1.4.2-1) ... Selecting previously unselected package r-cran-gtable. Preparing to unpack .../261-r-cran-gtable_0.3.0+dfsg-2_all.deb ... Unpacking r-cran-gtable (0.3.0+dfsg-2) ... Selecting previously unselected package r-cran-brio. Preparing to unpack .../262-r-cran-brio_1.1.1-1_arm64.deb ... Unpacking r-cran-brio (1.1.1-1) ... Selecting previously unselected package r-cran-ps. Preparing to unpack .../263-r-cran-ps_1.5.0-1_arm64.deb ... Unpacking r-cran-ps (1.5.0-1) ... Selecting previously unselected package r-cran-r6. Preparing to unpack .../264-r-cran-r6_2.5.0-1_all.deb ... Unpacking r-cran-r6 (2.5.0-1) ... Selecting previously unselected package r-cran-processx. Preparing to unpack .../265-r-cran-processx_3.4.5-1_arm64.deb ... Unpacking r-cran-processx (3.4.5-1) ... Selecting previously unselected package r-cran-callr. Preparing to unpack .../266-r-cran-callr_3.5.1-1_all.deb ... Unpacking r-cran-callr (3.5.1-1) ... Selecting previously unselected package r-cran-assertthat. Preparing to unpack .../267-r-cran-assertthat_0.2.1-2_all.deb ... Unpacking r-cran-assertthat (0.2.1-2) ... Selecting previously unselected package r-cran-cli. Preparing to unpack .../268-r-cran-cli_2.3.0-1_all.deb ... Unpacking r-cran-cli (2.3.0-1) ... Selecting previously unselected package r-cran-crayon. Preparing to unpack .../269-r-cran-crayon_1.4.0-1_all.deb ... Unpacking r-cran-crayon (1.4.0-1) ... Selecting previously unselected package r-cran-rprojroot. Preparing to unpack .../270-r-cran-rprojroot_2.0.2-1_all.deb ... Unpacking r-cran-rprojroot (2.0.2-1) ... Selecting previously unselected package r-cran-desc. Preparing to unpack .../271-r-cran-desc_1.2.0-3_all.deb ... Unpacking r-cran-desc (1.2.0-3) ... Selecting previously unselected package r-cran-rlang. Preparing to unpack .../272-r-cran-rlang_0.4.10-1_arm64.deb ... Unpacking r-cran-rlang (0.4.10-1) ... Selecting previously unselected package r-cran-ellipsis. Preparing to unpack .../273-r-cran-ellipsis_0.3.1-1_arm64.deb ... Unpacking r-cran-ellipsis (0.3.1-1) ... Selecting previously unselected package r-cran-evaluate. Preparing to unpack .../274-r-cran-evaluate_0.14-2_all.deb ... Unpacking r-cran-evaluate (0.14-2) ... Selecting previously unselected package r-cran-jsonlite. Preparing to unpack .../275-r-cran-jsonlite_1.7.2+dfsg-1_arm64.deb ... Unpacking r-cran-jsonlite (1.7.2+dfsg-1) ... Selecting previously unselected package r-cran-lifecycle. Preparing to unpack .../276-r-cran-lifecycle_0.2.0-2_all.deb ... Unpacking r-cran-lifecycle (0.2.0-2) ... Selecting previously unselected package r-cran-magrittr. Preparing to unpack .../277-r-cran-magrittr_2.0.1-1_arm64.deb ... Unpacking r-cran-magrittr (2.0.1-1) ... Selecting previously unselected package r-cran-prettyunits. Preparing to unpack .../278-r-cran-prettyunits_1.1.1-2_all.deb ... Unpacking r-cran-prettyunits (1.1.1-2) ... Selecting previously unselected package r-cran-withr. Preparing to unpack .../279-r-cran-withr_2.4.1-1_all.deb ... Unpacking r-cran-withr (2.4.1-1) ... Selecting previously unselected package r-cran-pkgbuild. Preparing to unpack .../280-r-cran-pkgbuild_1.2.0-1_all.deb ... Unpacking r-cran-pkgbuild (1.2.0-1) ... Selecting previously unselected package r-cran-rstudioapi. Preparing to unpack .../281-r-cran-rstudioapi_0.13-1_all.deb ... Unpacking r-cran-rstudioapi (0.13-1) ... Selecting previously unselected package r-cran-pkgload. Preparing to unpack .../282-r-cran-pkgload_1.1.0-1_arm64.deb ... Unpacking r-cran-pkgload (1.1.0-1) ... Selecting previously unselected package r-cran-praise. Preparing to unpack .../283-r-cran-praise_1.0.0-4_all.deb ... Unpacking r-cran-praise (1.0.0-4) ... Selecting previously unselected package r-cran-diffobj. Preparing to unpack .../284-r-cran-diffobj_0.3.2-1_arm64.deb ... Unpacking r-cran-diffobj (0.3.2-1) ... Selecting previously unselected package r-cran-fansi. Preparing to unpack .../285-r-cran-fansi_0.4.2-1_arm64.deb ... Unpacking r-cran-fansi (0.4.2-1) ... Selecting previously unselected package r-cran-utf8. Preparing to unpack .../286-r-cran-utf8_1.1.4-2_arm64.deb ... Unpacking r-cran-utf8 (1.1.4-2) ... Selecting previously unselected package r-cran-vctrs. Preparing to unpack .../287-r-cran-vctrs_0.3.6-1_arm64.deb ... Unpacking r-cran-vctrs (0.3.6-1) ... Selecting previously unselected package r-cran-pillar. Preparing to unpack .../288-r-cran-pillar_1.4.7-1_all.deb ... Unpacking r-cran-pillar (1.4.7-1) ... Selecting previously unselected package r-cran-pkgconfig. Preparing to unpack .../289-r-cran-pkgconfig_2.0.3-2_all.deb ... Unpacking r-cran-pkgconfig (2.0.3-2) ... Selecting previously unselected package r-cran-tibble. Preparing to unpack .../290-r-cran-tibble_3.0.6+dfsg-1_arm64.deb ... Unpacking r-cran-tibble (3.0.6+dfsg-1) ... Selecting previously unselected package r-cran-rematch2. Preparing to unpack .../291-r-cran-rematch2_2.1.2-2_all.deb ... Unpacking r-cran-rematch2 (2.1.2-2) ... Selecting previously unselected package r-cran-waldo. Preparing to unpack .../292-r-cran-waldo_0.2.3-2_all.deb ... Unpacking r-cran-waldo (0.2.3-2) ... Selecting previously unselected package r-cran-testthat. Preparing to unpack .../293-r-cran-testthat_3.0.1-1_arm64.deb ... Unpacking r-cran-testthat (3.0.1-1) ... Selecting previously unselected package r-cran-isoband. Preparing to unpack .../294-r-cran-isoband_0.2.3-2_arm64.deb ... Unpacking r-cran-isoband (0.2.3-2) ... Selecting previously unselected package r-cran-mass. Preparing to unpack .../295-r-cran-mass_7.3-53.1-1_arm64.deb ... Unpacking r-cran-mass (7.3-53.1-1) ... Selecting previously unselected package r-cran-lattice. Preparing to unpack .../296-r-cran-lattice_0.20-41-1+b1_arm64.deb ... Unpacking r-cran-lattice (0.20-41-1+b1) ... Selecting previously unselected package r-cran-nlme. Preparing to unpack .../297-r-cran-nlme_3.1.152-1_arm64.deb ... Unpacking r-cran-nlme (3.1.152-1) ... Selecting previously unselected package r-cran-matrix. Preparing to unpack .../298-r-cran-matrix_1.3-2-1_arm64.deb ... Unpacking r-cran-matrix (1.3-2-1) ... Selecting previously unselected package r-cran-mgcv. Preparing to unpack .../299-r-cran-mgcv_1.8-34-1_arm64.deb ... Unpacking r-cran-mgcv (1.8-34-1) ... Selecting previously unselected package r-cran-farver. Preparing to unpack .../300-r-cran-farver_2.0.3-1+b1_arm64.deb ... Unpacking r-cran-farver (2.0.3-1+b1) ... Selecting previously unselected package r-cran-labeling. Preparing to unpack .../301-r-cran-labeling_0.4.2-1_all.deb ... Unpacking r-cran-labeling (0.4.2-1) ... Selecting previously unselected package r-cran-colorspace. Preparing to unpack .../302-r-cran-colorspace_2.0-0+dfsg-1_arm64.deb ... Unpacking r-cran-colorspace (2.0-0+dfsg-1) ... Selecting previously unselected package r-cran-munsell. Preparing to unpack .../303-r-cran-munsell_0.5.0-2_all.deb ... Unpacking r-cran-munsell (0.5.0-2) ... Selecting previously unselected package r-cran-rcolorbrewer. Preparing to unpack .../304-r-cran-rcolorbrewer_1.1-2-3_all.deb ... Unpacking r-cran-rcolorbrewer (1.1-2-3) ... Selecting previously unselected package r-cran-viridislite. Preparing to unpack .../305-r-cran-viridislite_0.3.0-4_all.deb ... Unpacking r-cran-viridislite (0.3.0-4) ... Selecting previously unselected package r-cran-scales. Preparing to unpack .../306-r-cran-scales_1.1.1-1_all.deb ... Unpacking r-cran-scales (1.1.1-1) ... Selecting previously unselected package r-cran-ggplot2. Preparing to unpack .../307-r-cran-ggplot2_3.3.3+dfsg-1_all.deb ... Unpacking r-cran-ggplot2 (3.3.3+dfsg-1) ... Selecting previously unselected package r-cran-gridbase. Preparing to unpack .../308-r-cran-gridbase_0.4-7-5_all.deb ... Unpacking r-cran-gridbase (0.4-7-5) ... Selecting previously unselected package libvcflib-tools. Preparing to unpack .../309-libvcflib-tools_1.0.2+dfsg-2_arm64.deb ... Unpacking libvcflib-tools (1.0.2+dfsg-2) ... Selecting previously unselected package protobuf-compiler. Preparing to unpack .../310-protobuf-compiler_3.12.4-1+deb11u1_arm64.deb ... Unpacking protobuf-compiler (3.12.4-1+deb11u1) ... Selecting previously unselected package pv. Preparing to unpack .../311-pv_1.6.6-1_arm64.deb ... Unpacking pv (1.6.6-1) ... Selecting previously unselected package rapidjson-dev. Preparing to unpack .../312-rapidjson-dev_1.1.0+dfsg2-7_all.deb ... Unpacking rapidjson-dev (1.1.0+dfsg2-7) ... Selecting previously unselected package raptor2-utils. Preparing to unpack .../313-raptor2-utils_2.0.14-1.2_arm64.deb ... Unpacking raptor2-utils (2.0.14-1.2) ... Selecting previously unselected package rasqal-utils. Preparing to unpack .../314-rasqal-utils_0.9.33-0.1_arm64.deb ... Unpacking rasqal-utils (0.9.33-0.1) ... Selecting previously unselected package rs. Preparing to unpack .../315-rs_20200313-1_arm64.deb ... Unpacking rs (20200313-1) ... Selecting previously unselected package samtools. Preparing to unpack .../316-samtools_1.11-1_arm64.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package tabix. Preparing to unpack .../317-tabix_1.11-4_arm64.deb ... Unpacking tabix (1.11-4) ... Selecting previously unselected package xxd. Preparing to unpack .../318-xxd_2%3a8.2.2434-3+deb11u1_arm64.deb ... Unpacking xxd (2:8.2.2434-3+deb11u1) ... Setting up media-types (4.0.0) ... Setting up libpcrecpp0v5:arm64 (2:8.39-13) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up libgraphite2-3:arm64 (1.3.14-1) ... Setting up libsimde-dev (0.7.2-4) ... Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-2) ... Setting up libpixman-1-0:arm64 (0.40.0-1.1~deb11u1) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up libboost1.74-dev:arm64 (1.74.0-9) ... Setting up libpixman-1-dev:arm64 (0.40.0-1.1~deb11u1) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libpcre16-3:arm64 (2:8.39-13) ... Setting up libicu67:arm64 (67.1-7) ... Setting up libdatrie1:arm64 (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up ncal (12.1.7+nmu3) ... Setting up gawk (1:5.1.0-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up bwa (0.7.17-6+b1) ... Setting up libboost-program-options1.74.0:arm64 (1.74.0-9) ... Setting up unzip (6.0-26+deb11u1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up liblab-gamut1:arm64 (2.42.2-5) ... Setting up libyajl2:arm64 (2.1.0-3+deb11u2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsmithwaterman0 (0.0+git20160702.2610e25-11) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3+deb11u1) ... Setting up libsepol1-dev:arm64 (3.1-1) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up m4 (1.4.18-5) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libprotobuf23:arm64 (3.12.4-1+deb11u1) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libjemalloc2:arm64 (5.2.1-3) ... Setting up libffi-dev:arm64 (3.3-6) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libpthread-stubs0-dev:arm64 (0.4-1) ... Setting up libfml0:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up libfastahack0 (1.0.0+dfsg-7) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up libpcre2-16-0:arm64 (10.36-2+deb11u1) ... Setting up xxd (2:8.2.2434-3+deb11u1) ... Setting up rapidjson-dev (1.1.0+dfsg2-7) ... Setting up libjansson4:arm64 (2.13.1-1.1) ... Setting up libboost-program-options1.74-dev:arm64 (1.74.0-9) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libfastahack-dev (1.0.0+dfsg-7) ... Setting up libosp5 (1.5.2-13+b2) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jan 7 18:51:37 UTC 2024. Universal Time is now: Sun Jan 7 18:51:37 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgts-0.7-5:arm64 (0.7.6+darcs121130-4+b1) ... Setting up libjemalloc-dev (5.2.1-3) ... Setting up libbackward-cpp-dev (1.5-2) ... Setting up xtrans-dev (1.4.0-1) ... Setting up zip (3.0-12) ... Setting up libprotobuf-lite23:arm64 (3.12.4-1+deb11u1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:arm64 (4.8.10-1) ... Setting up libpcre2-32-0:arm64 (10.36-2+deb11u1) ... Setting up libblas3:arm64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libglib2.0-data (2.66.8-1) ... Setting up libgmpxx4ldbl:arm64 (2:6.2.1+dfsg-1+deb11u1) ... Setting up libuv1:arm64 (1.40.0-2) ... Setting up libexpat1-dev:arm64 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libboost-program-options-dev:arm64 (1.74.0.3) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up uuid-dev:arm64 (2.36.1-8+deb11u1) ... Setting up libpathplan4:arm64 (2.42.2-5) ... Setting up libprotoc23:arm64 (3.12.4-1+deb11u1) ... Setting up libann0 (1.1.2+doc-7) ... Setting up libncurses6:arm64 (6.2+20201114-2+deb11u2) ... Setting up libtsl-hopscotch-map-dev (2.3.0-1) ... Setting up libfribidi0:arm64 (1.0.8-2+deb11u1) ... Setting up bsdmainutils (12.1.7+nmu3) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up libpcre32-3:arm64 (2:8.39-13) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1+deb11u2) ... Setting up icu-devtools (67.1-7) ... Setting up liblz4-dev:arm64 (1.9.3-2) ... Setting up pkg-config (0.29.2-1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcre2-posix2:arm64 (10.36-2+deb11u1) ... Setting up libdisorder-dev:arm64 (0.0.2+git20130809.8062ee1-2) ... Setting up libltdl7:arm64 (2.4.6-15) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up libmhash2:arm64 (0.9.9.9-9) ... Setting up libyajl-dev:arm64 (2.1.0-3+deb11u2) ... Setting up liblzma-dev:arm64 (5.2.5-2.1~deb11u1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up pv (1.6.6-1) ... Setting up librhash0:arm64 (1.4.1-2) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up bison (2:3.7.5+dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up sgml-base (1.30) ... Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libcdt5:arm64 (2.42.2-5) ... Setting up libcgraph6:arm64 (2.42.2-5) ... Setting up libtiff5:arm64 (4.2.0-1+deb11u4) ... Setting up libdivsufsort3:arm64 (2.0.1-5) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:arm64 (0.11.3-1+deb11u1) ... Setting up libdeflate-dev:arm64 (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libssw0:arm64 (1.1-13) ... Setting up libicu-dev:arm64 (67.1-7) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7+deb11u4) ... 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:arm64 (2.13.1-1.1) ... Setting up libonig5:arm64 (6.9.6-1.1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libbrotli-dev:arm64 (1.0.9-2+b2) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up libdivsufsort-dev:arm64 (2.0.1-5) ... Setting up rs (20200313-1) ... Setting up libbz2-dev:arm64 (1.0.8-4) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libblkid-dev:arm64 (2.36.1-8+deb11u1) ... Setting up libice6:arm64 (2:1.0.10-1) ... Setting up libdw1:arm64 (0.183-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up flex (2.6.4-8) ... Setting up liblapack3:arm64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.2+20201114-2+deb11u2) ... Setting up libxcb1:arm64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up libgmp-dev:arm64 (2:6.2.1+dfsg-1+deb11u1) ... Setting up libxau-dev:arm64 (1:1.0.9-1) ... Setting up libpcre2-dev:arm64 (10.36-2+deb11u1) ... Setting up protobuf-compiler (3.12.4-1+deb11u1) ... Setting up libice-dev:arm64 (2:1.0.10-1) ... Setting up libssw-dev:arm64 (1.1-13) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2+deb11u1) ... Setting up libxcb-render0:arm64 (1.14-3) ... Setting up libselinux1-dev:arm64 (3.1-3) ... Setting up libjq1:arm64 (1.6-2.1) ... Setting up libpcre3-dev:arm64 (2:8.39-13) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libpng-dev:arm64 (1.6.37-3) ... Setting up bc (1.07.1-2+b2) ... Setting up libglib2.0-bin (2.66.8-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3+deb11u1) ... Setting up fastahack (1.0.0+dfsg-7) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+deb11u9) ... Setting up libxcb-shm0:arm64 (1.14-3) ... Setting up opensp (1.5.2-13+b2) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3+deb11u9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libprotobuf-dev:arm64 (3.12.4-1+deb11u1) ... Setting up help2man (1.48.1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up libxml2-dev:arm64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libllvm11:arm64 (1:11.0.1-2) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1+deb11u1) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up libelf-dev:arm64 (0.183-1) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libgvpr2:arm64 (2.42.2-5) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libprotoc-dev:arm64 (3.12.4-1+deb11u1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up jq (1.6-2.1) ... Setting up procps (2:3.3.17-5) ... Setting up libncurses5-dev:arm64 (6.2+20201114-2+deb11u2) ... Setting up libxslt1.1:arm64 (1.1.34-4+deb11u1) ... Setting up libcurl4:arm64 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:arm64 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libasm1:arm64 (0.183-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libmount-dev:arm64 (2.36.1-8+deb11u1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpaper1:arm64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up elfutils (0.183-1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libxcb1-dev:arm64 (1.14-3) ... Setting up libxslt1-dev:arm64 (1.1.34-4+deb11u1) ... Setting up libxpm4:arm64 (1:3.5.12-1.1~deb11u1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libsm-dev:arm64 (2:1.2.3-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up xsltproc (1.1.34-4+deb11u1) ... Setting up libraptor2-0:arm64 (2.0.14-1.2) ... Setting up raptor2-utils (2.0.14-1.2) ... Setting up libx11-dev:arm64 (2:1.7.2-1+deb11u1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up python3 (3.9.2-3) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libdw-dev:arm64 (0.183-1) ... Setting up samtools (1.11-1) ... Setting up libfreetype-dev:arm64 (2.10.4+dfsg-1+deb11u1) ... Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up libxcb-shm0-dev:arm64 (1.14-3) ... Setting up doxygen (1.9.1-1) ... Setting up libxcb-render0-dev:arm64 (1.14-3) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up libxext-dev:arm64 (2:1.3.3-1.1) ... Setting up python3-lxml:arm64 (4.6.3+dfsg-0.1+deb11u1) ... Setting up libtabixpp0:arm64 (1.1.0-4) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libraptor2-dev (2.0.14-1.2) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up libxrender-dev:arm64 (1:0.9.10-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up libglib2.0-dev-bin (2.66.8-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.2-2) ... Setting up libxmu6:arm64 (2:1.1.2-2+b3) ... Setting up libtk8.6:arm64 (8.6.11-2) ... Setting up librasqal3:arm64 (0.9.33-0.1) ... Setting up libpango-1.0-0:arm64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up librasqal3-dev (0.9.33-0.1) ... Setting up libxaw7:arm64 (2:1.0.13-1.1) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up libfreetype6-dev:arm64 (2.10.4+dfsg-1+deb11u1) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up libglib2.0-dev:arm64 (2.66.8-1) ... Setting up librdf0:arm64 (1.0.17-1.1+b1) ... Setting up libgd3:arm64 (2.3.0-2) ... Setting up librdf0-dev (1.0.17-1.1+b1) ... Setting up libvcflib1:arm64 (1.0.2+dfsg-2) ... Setting up libtabixpp-dev:arm64 (1.1.0-4) ... Setting up libcairo-gobject2:arm64 (1.16.0-5) ... Setting up libpangoft2-1.0-0:arm64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:arm64 (1.46.2-3) ... Setting up libvcflib-dev:arm64 (1.0.2+dfsg-2) ... Setting up libcairo-script-interpreter2:arm64 (1.16.0-5) ... Setting up rasqal-utils (0.9.33-0.1) ... Setting up libfontconfig-dev:arm64 (2.13.1-4.2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up libgvc6 (2.42.2-5) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up libcairo2-dev:arm64 (1.16.0-5) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up graphviz (2.42.2-5) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up libfontconfig1-dev:arm64 (2.13.1-4.2) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-plyr (1.8.6-2) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up libvcflib-tools (1.0.2+dfsg-2) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-9) ... Setting up docbook (4.5-6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-to-man (1:2.0.0-45) ... Setting up gtk-doc-tools (1.33.2-1) ... Processing triggers for ca-certificates (20210119) ... 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 arm64 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 -j12 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' cd cutest && make clean cd quicktree_1.1 && make clean rm -rf ../bin ../lib make[5]: Entering 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/C' 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 -j12 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: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 dh_auto_build -- all test/build_graph bin/shuf make -j12 "INSTALL=install --strip-program=true" 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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* cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.30.0+ds/include rm -Rf include/boost make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gssw' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc touch lib/cleaned_old_boost 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c cp -r deps/sparsepp/sparsepp include/ rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all Library will be installed in '/build/reproducible-path/vg-1.30.0+ds' touch lib/cleaned_old_protobuf_v003 rm -Rf include/dynamic.hpp include/dynamic # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.30.0+ds/include/ make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make cd quicktree_1.1 && make all CC="gcc -std=c99" . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d bin ]; then mkdir -p bin; fi 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c if [ ! -d obj ]; then mkdir -p obj; fi CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (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. 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/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.30.0+ds/include/ -- Setting build type to 'Debug' as none was specified. if [ ! -d lib ]; then mkdir -p lib; fi cp deps/sha1/*.h* /build/reproducible-path/vg-1.30.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /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' cp -r deps/dozeu/simde 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/* find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.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/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -- The C compiler identification is GNU 10.2.1 ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -- The C compiler identification is GNU 10.2.1 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 -- The CXX compiler identification is GNU 10.2.1 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 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- The CXX compiler identification is GNU 10.2.1 gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- The C compiler identification is GNU 10.2.1 ar rc cuTest.a *.o ranlib cuTest.a -- Detecting CXX compiler ABI info rm -f *.o mv cuTest.a ../../lib/ gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c cp CuTest.h ../../lib/ gcc -std=c99 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -- Detecting C compiler ABI info - done ./src/tree.c: In function ‘read_newhampshire_Tnode’: -- Check for working C compiler: /usr/bin/gcc - skipped ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ diff: ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ include/vg_environment_version.hpp: No such file or directory -- Detecting C compile features -- Detecting C compile features - done -- 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 . ./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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info ln -s `which shuf` bin/shuf . ./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 . ./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 -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done -- Generating done -- 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 make -f CMakeFiles/Makefile2 all . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac -- Detecting C compiler ABI info - done make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' -- Detecting CXX compiler ABI info - done make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend -- 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 -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done 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= Building in Debug mode -- Configuring done Scanning dependencies of target handlegraph_objs make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' -- Generating done -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build 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]: Entering 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/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend 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= . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am Scanning dependencies of target cw-bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' 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' [ 7%] Building CXX object CMakeFiles/cw-bwt.dir/cw-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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/cw-bwt.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 rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/vg/io/ -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs 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 . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./autogen.sh || true 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 ./autogen.sh: 22: [[: not found 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 cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h -- The CXX compiler identification is GNU 10.2.1 cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Detecting CXX compiler ABI info 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 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 cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/structures' mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h 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/ [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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/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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h -- Detecting CXX compiler ABI info - done cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp -- Check for working CXX compiler: /usr/bin/g++ - skipped mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h -- Detecting CXX compile features -- Detecting CXX compile features - done cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/progress_bar' [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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/sonLibExcept.h ../lib/sonLibExcept.h.tmp make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend 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= mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h Scanning dependencies of target rle_bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/rle_bwt.cpp 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 In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 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 -- 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 cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") cp inc/stMatrix.h ../lib/stMatrix.h.tmp -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp -- Looking for C++ include cstdio - found mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h -- Found Doxygen: /usr/bin/doxygen (found version "1.9.1") found components: doxygen dot 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.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/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 -- Configuring 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -- Generating done -- 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 libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' make -f CMakeFiles/Makefile2 sdsl -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 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/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/aarch64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/aarch64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 libtoolize: copying file 'acinclude.d/ltoptions.m4' 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= [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o [ 32%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp -- Found htslib, version 1.11-4 /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 Scanning dependencies of target sdsl 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp libtoolize: copying file 'acinclude.d/ltsugar.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 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)) { | ^ -- Checking for module 'jansson' libtoolize: copying file 'acinclude.d/ltversion.m4' -- Found jansson, version 2.13.1 [ 38%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio libtoolize: copying file 'acinclude.d/lt~obsolete.m4' 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/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 -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/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/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[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/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= Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target 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' 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Built target link_target 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' 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= Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph 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' [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix 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 | ^~~~ /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] 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 [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 /usr/bin/cmake -E touch /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [ 9%] No patch 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-patch /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 | } | ^ [ 11%] 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" /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (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 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.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/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 -- The C compiler identification is GNU 10.2.1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting C compile features - done -- 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -- Detecting CXX 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- 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 [ 14%] 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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= /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::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 | } | ^ Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Scanning dependencies of target handlegraph_objs 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 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' 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -O3 -g -fPIC -std=gnu++14 -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 [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.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/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 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:697:75: note: declared here 697 | 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, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | 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, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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' [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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/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 | ^~~~ 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, 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/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /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))) | ~~^~~~~~~~~~~ In file included 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/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 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/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 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/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 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/int_vector.hpp:24, 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/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))) | ~~^~~~~~~~~~~ In file included 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/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.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 | ^~~~ /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp /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[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_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= Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Scanning dependencies of target handlegraph_static 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' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, 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/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /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))) | ~~^~~~~~~~~~~ In file included 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/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 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/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 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/int_vector.hpp:24, 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/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))) | ~~^~~~~~~~~~~ In file included 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/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, 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/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 | ^~~~~~~~~ In file included 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/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp /usr/bin/ranlib libhandlegraph.a 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' [ 66%] Built target handlegraph_static 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= Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Scanning dependencies of target handlegraph_shared 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' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 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 [100%] Built target handlegraph_shared 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' configure.ac:3: installing './missing' [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 16%] 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 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 | ^~~~ cluster/Makefile.am: installing './depcomp' /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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 -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' [ 21%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -o cw-bwt 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' [ 66%] Built target handlegraph_static 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' [100%] Built target handlegraph_shared 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_lcp.cpp.o make -f CMakeFiles/Makefile2 preinstall 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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[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' make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [ 21%] Built target cw-bwt Install the project... make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend /usr/bin/cmake -P cmake_install.cmake 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= -- 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/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/expanding_overlay_graph.hpp -- 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/path_position_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/path_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/deletable_handle_graph.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/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.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 Scanning dependencies of target h0_lz77 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 make[5]: Entering 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 [ 28%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o [ 19%] Completed 'handlegraph' /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/h0_lz77.cpp /usr/bin/cmake -E make_directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.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 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/libvgio' [ 19%] Built target handlegraph [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 21%] 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 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/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= Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static 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' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o 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 | ^~~~ /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/vg.pb.cc 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 [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a thread-safe mkdir -p... [ 35%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt 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 checking whether make supports nested variables... yes [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp ar rc /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.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/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ranlib /build/reproducible-path/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a checking whether the C++ compiler works... make[5]: Leaving 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/sublinear-Li-Stephens' [ 35%] Built target rle_bwt make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend 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= Scanning dependencies of target benchmark make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 [ 42%] Building CXX object CMakeFiles/benchmark.dir/benchmark.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/benchmark.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking whether make supports the include directive... [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp 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 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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend 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= checking build system type... Scanning dependencies of target rle_lz77_v2 make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Leaving 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/rle_lz77_v1.dir/DependInfo.cmake --color= make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering 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 Scanning dependencies of target rle_lz77_v1 [ 50%] 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' /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -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 make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [ 57%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.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_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static 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/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.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_shared.dir/DependInfo.cmake --color= aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... Scanning dependencies of target handlegraph_shared 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/build printf checking for gcc... gcc make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 checking whether we are using the GNU C compiler... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: 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/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph' yes checking whether gcc accepts -g... make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend 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= Scanning dependencies of target debug 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 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 | ^~~~ make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' /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 accept ISO C89... [ 64%] Building CXX object CMakeFiles/debug.dir/debug.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/debug.cpp 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 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... /bin/sed checking for grep that handles long lines and -e... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... 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 BSD- or MS-compatible name lister (nm)... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 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 1572864 ranlib sonLib.a rm *.o checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r 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... 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 @ 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... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o checking for ANSI C header files... /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 [ 71%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' yes [ 71%] Built target debug checking for sys/types.h... [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 sys/stat.h... yes checking for stdlib.h... yes checking for string.h... [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp yes checking for memory.h... yes 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 | ^~~~ checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... [ 78%] Linking CXX executable benchmark /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark yes checking for dlfcn.h... yes make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' checking for objdir... [ 78%] Built target benchmark .libs [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 if gcc supports -fno-rtti -fno-exceptions... [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp 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... [ 85%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 yes checking whether -lc should be explicitly linked in... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' 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 | ^~~~ [ 85%] Built target h0_lz77 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 no checking dynamic linker characteristics... 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 | ^~~~ [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp 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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes 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 whether the g++ linker (/usr/bin/ld) supports shared libraries... yes [ 30%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 [ 92%] Linking CXX executable rle_lz77_v1 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [ 92%] Built target rle_lz77_v1 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... [100%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 yes checking if g++ static flag -static works... 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 | ^~~~ mv ../bin/sonLibTests.tmp ../bin/sonLibTests 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 yes checking if g++ supports -c -o file.o... make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/build' [100%] Built target rle_lz77_v2 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 [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o 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. 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp # Otherwise we get dynamic.hpp without its deps 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 | ^~~~ mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.30.0+ds/deps/DYNAMIC/include/* include/dynamic [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) 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... [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -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 ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm yes checking whether the Boost::Program_Options library is available... mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm 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= 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 instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest 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' [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o [ 35%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest 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' [ 38%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.30.0+ds/lib/lib3edgeconnected.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 [ 40%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all yes make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 42%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp checking for exit in -lboost_program_options... 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 | ^~~~ [ 45%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 47%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 ar rc 3EdgeConnected.a *.o yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm yes checking for joinable pthread attribute... [ 50%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 52%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... [ 54%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 57%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I .//../sonLib/lib/ -c impl/*.c yes [ 59%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp checking that generated files are newer than configure... done configure: creating ./config.status /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:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 61%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 64%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -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 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 instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [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 [ 66%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ /usr/bin/ranlib libsdsl.a cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.30.0+ds/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a 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 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' 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 -- 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 [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -- 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 /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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 -- 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 [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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[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! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/reproducible-path/vg-1.30.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c algorithms.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c dbg.cpp [ 85%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake [ 88%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 88%] Built target vgio_static /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:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | 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:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 92%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 95%] 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c files.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/pinchesAndCacti' . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/reproducible-path/vg-1.30.0+ds/lib 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' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c bwtmerge.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c cached_gbwt.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c files.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c gbwt.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c internal.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c gcsa.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c support.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c test.cpp config.status: creating cluster/Makefile config.status: creating library/Makefile In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating libvw.pc /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c internal.cpp config.status: creating vowpalwabbit/config.h In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c lcp.cpp config.status: executing depfiles commands In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib -Wl,-rpath,/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/aarch64-linux-gnu/libprotobuf.so -lhts -ljansson -lhandlegraph -ldl In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 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/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]: 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' [ 0%] Built target link_target 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' 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/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph 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' 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= 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' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static 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= In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /build/reproducible-path/vg-1.30.0+ds/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/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build /build/reproducible-path/vg-1.30.0+ds/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libvgio.so -- Set runtime path of "/build/reproducible-path/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.30.0+ds/include -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.30.0+ds/include:/build/reproducible-path/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.30.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c utils.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c path_graph.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c build_ri.cpp config.status: executing libtool commands g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/reproducible-path/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c support.cpp checking whether make supports nested variables... yes In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c metadata_tool.cpp 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... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ no /usr/bin/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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c remove_seq.cpp checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c utils.cpp yes (GNU style) checking dependency style of g++... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -E In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for gcc... gcc rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.30.0+ds/include . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o yes checking for BSD- or MS-compatible name lister (nm)... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r 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... ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 no checking how to run the C preprocessor... gcc -E /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 checking for ANSI C header files... /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 yes checking for sys/types.h... /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 yes checking for sys/stat.h... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o yes make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwt' checking for stdlib.h... . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/reproducible-path/vg-1.30.0+ds/lib yes 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' make[3]: Entering directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c algorithms.cpp checking for string.h... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o yes checking for memory.h... yes g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c gbwtgraph.cpp 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) supports shared libraries... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c gfa.cpp 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 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c path_cover.cpp checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/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/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c utils.cpp yes checking if g++ supports -c -o file.o... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -c gfa2gbwt.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) 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 ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... In file included from /build/reproducible-path/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/reproducible-path/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/reproducible-path/vg-1.30.0+ds/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/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/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/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/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/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gcsa2' 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" 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' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la 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 ../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' 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/reproducible-path/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds/deps/libbdsg' depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_args.h:7, from main.cc:13: feature_group.h: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 global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h: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:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from unique_sort.cc:6: feature_group.h: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:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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 cache.cc:6: feature_group.h: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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from cache.h:9, from cache.cc:6: feature_group.h: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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: 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:131:56: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.cc:23: feature_group.h: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 global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h: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 global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: 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 ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from multiclass.cc:3: feature_group.h: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 global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h: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 global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from global_data.cc:14: feature_group.h: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 global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h: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 global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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 simple_label.cc:6: feature_group.h: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 simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h: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 simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from oaa.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from oaa.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from multilabel_oaa.cc:8: feature_group.h: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 multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h: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 multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from boosting.cc:22: feature_group.h: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 boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h: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 boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from ect.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from ect.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from marginal.cc:2: feature_group.h: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 marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h: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 marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from autolink.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from autolink.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from binary.cc:2: feature_group.h: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 binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h: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 binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from lrq.cc:3: feature_group.h: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 lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h: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 lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_adf.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:109:13: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: 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 label_dictionary.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from label_dictionary.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from label_dictionary.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc: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:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: 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::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:94:38: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: 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 label_dictionary.cc: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:94:38: 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, from label_dictionary.cc:1: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from csoaa.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from csoaa.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: 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 = 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:895:56: 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, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from cb_adf.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from cb_adf.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h: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:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from cb.cc:8: feature_group.h: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:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from cb_algs.cc:8: feature_group.h: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 global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.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:1265:29: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: 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 = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: 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, from vw.h:15, from search.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from search.cc: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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from search.cc: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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: 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 search.cc:9: 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:620:29: 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 | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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:1009:64: 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 | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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:1084:94: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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:1097:36: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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:1517:47: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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:1695:65: 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 | ^~~~~~~~~~~~~ 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:27, from vw.h:15, from search.cc:9: 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:1295:65: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: 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:124:75: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search_meta.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from search_meta.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: 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 search_meta.cc:9: 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:108:20: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: 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:109:17: 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: 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:110:22: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, 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, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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_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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: 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::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:442:28: 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++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ 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: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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: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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h: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 global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_example.cc: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} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from parse_example.h:9, from parse_example.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from scorer.cc:3: feature_group.h: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 scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h: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 scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from accumulate.cc:15: feature_group.h: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 global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h: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 global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from learner.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from parser.h:9, from learner.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from mwt.cc:6: feature_group.h: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 global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo noop.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from lda_core.cc: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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | 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:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from mf.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from mf.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from accumulate.h:8, from bfgs.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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from noop.cc:8: feature_group.h: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 noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h: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 noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from print.cc: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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parser.cc:48: feature_group.h: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 parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from loss_functions.cc:13: feature_group.h: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 global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h: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 global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: 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:106:50: 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)); | ^ 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:115:54: 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)); | ^ 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. | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from nn.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from example.h:17, from reductions.h:11, from nn.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from nn.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from confidence.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from confidence.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from bs.cc:13: feature_group.h: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 bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h: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 bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from cbify.cc:2: feature_group.h: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 cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h: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 cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from explore_eval.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from explore_eval.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from topk.cc:10: feature_group.h: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 topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h: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 topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from log_multi.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from log_multi.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: 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 = 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:93:17: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from recall_tree.cc:12: feature_group.h: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 recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h: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 recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: 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 recall_tree.cc:12: 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:94:31: 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 | ^~~~ 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 = 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:139:39: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from active.cc:2: feature_group.h: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 active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from active.cc:2: feature_group.h: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 active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from active_cover.cc:2: feature_group.h: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 active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h: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 active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from cs_active.cc:2: feature_group.h: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 cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h: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 cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: 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 = 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:347:151: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from best_constant.h:3, from best_constant.cc: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} | ^~~~~~~~~~~~~ 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:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from kernel_svm.cc:18: feature_group.h: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 parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from lrqfa.cc:2: feature_group.h: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 lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h: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 lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from interact.cc:8: feature_group.h: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 interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h: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 interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from interactions.h:3, from interactions.cc: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} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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_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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw_validate.cc:6: feature_group.h: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 global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h: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 global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from vw.h:15, from gen_cs_example.cc:8: feature_group.h: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 global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from audit_regressor.cc:7: feature_group.h: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 audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h: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 audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo baseline.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from cb_explore_adf.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from cb_explore_adf.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h: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 global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h: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 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from baseline.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from baseline.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: 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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc: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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from cb_explore.cc: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} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from cb_explore.cc: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} | ^~~~~~~~~~~~~ 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 = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 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:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ 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 /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_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, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ 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 = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; 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, from classweight.cc:2: feature_group.h: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 classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ 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 example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h: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 classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/reproducible-path/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/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 -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -pthread -pthread -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/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 -L/build/reproducible-path/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -pthread -pthread -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -pthread 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -pthread 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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -pthread /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 /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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -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 -pthread 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/ . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/reproducible-path/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && 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 -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/reproducible-path/vg-1.30.0+ds/lib /build/reproducible-path/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/reproducible-path/vg-1.30.0+ds/include -isystem /build/reproducible-path/vg-1.30.0+ds/include -I. -I/build/reproducible-path/vg-1.30.0+ds/src -I/build/reproducible-path/vg-1.30.0+ds/src/unittest -I/build/reproducible-path/vg-1.30.0+ds/src/subcommand -I/build/reproducible-path/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/aarch64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/reproducible-path/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/reproducible-path/vg-1.30.0+ds/lib /build/reproducible-path/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' cp bin/vg debian/help/ PATH=$PATH:/build/reproducible-path/vg-1.30.0+ds/debian/help \ help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' dh_auto_build -- docs make -j12 "INSTALL=install --strip-program=true" docs make[2]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' doxygen warning: Tag 'TCL_SUBST' at line 237 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1001 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 2054 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 2076 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source 'deps/libbdsg/src' does not exist warning: tag INPUT: input source 'deps/libbdsg/include/bdsg' does not exist warning: source 'deps/libbdsg/src' is not a readable file or directory... skipping. warning: source 'deps/libbdsg/include/bdsg' is not a readable file or directory... skipping. Adding custom extension mapping: 'proto' will be treated as language 'c++' Doxygen version used: 1.9.1 Notice: Output directory 'doc/doxygen' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/src Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/src/algorithms Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/src/io Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/src/subcommand Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io Searching for files in directory /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/aligner.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/aligner.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/alignment.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/alignment.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/alignment.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/alignment.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/annotation.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/annotation.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/augment.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/augment.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/augment.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/augment.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/benchmark.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/build_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/build_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/build_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/build_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cactus.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cactus.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cactus.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cactus.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cactus_snarl_finder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cactus_snarl_finder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cactus_snarl_finder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cactus_snarl_finder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/chunker.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/chunker.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/chunker.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/chunker.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cluster.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cluster.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/cluster.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/cluster.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/colors.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/colors.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/constructor.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/constructor.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/constructor.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/constructor.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/convert.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/convert.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/crash.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/crash.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/crash.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/crash.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dagified_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dagified_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dagified_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dagified_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/deconstructor.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/deconstructor.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/deconstructor.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/deconstructor.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/deletion_aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/deletion_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/deletion_aligner.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/deletion_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dinucleotide_machine.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dinucleotide_machine.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dinucleotide_machine.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dinucleotide_machine.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dozeu_interface.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dozeu_interface.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dozeu_interface.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dozeu_interface.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dozeu_pinning_overlay.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dozeu_pinning_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/dozeu_pinning_overlay.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/dozeu_pinning_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/endianness.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/endianness.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/entropy.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/entropy.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/entropy.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/entropy.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/extra_node_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/extra_node_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/extra_node_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/extra_node_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/feature_set.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/feature_set.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/feature_set.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/feature_set.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/filter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/filter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/filter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/filter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/flow_sort.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/flow_sort.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/flow_sort.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/flow_sort.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/funnel.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/funnel.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/funnel.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/funnel.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gapless_extender.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gapless_extender.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gapless_extender.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gapless_extender.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gbwt_helper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gbwt_helper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gbwt_helper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gbwt_helper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genome_state.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genome_state.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genome_state.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genome_state.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genotyper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genotyper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/genotyper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/genotyper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gfa.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gfa.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gfa.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gfa.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gff_reader.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gff_reader.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/gff_reader.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/gff_reader.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph_caller.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph_caller.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph_caller.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph_caller.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph_synchronizer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph_synchronizer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/graph_synchronizer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/graph_synchronizer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/handle.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/handle.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotype_indexer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_indexer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotype_indexer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_indexer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotypes.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotypes.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/haplotypes.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/haplotypes.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/hash_map.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/hash_map.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/homogenizer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/homogenizer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/homogenizer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/homogenizer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/identity_overlay.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/identity_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/identity_overlay.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/identity_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/incremental_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/incremental_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/incremental_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/incremental_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/index_manager.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/index_manager.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/index_manager.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/index_manager.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/index_registry.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/index_registry.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/index_registry.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/index_registry.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/indexed_vg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/indexed_vg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/indexed_vg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/indexed_vg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/integrated_snarl_finder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/integrated_snarl_finder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/integrated_snarl_finder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/integrated_snarl_finder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/kmer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mapper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mapper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mapper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mapper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mcmc_caller.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mcmc_caller.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mcmc_caller.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mcmc_caller.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mcmc_genotyper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mcmc_genotyper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mcmc_genotyper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mcmc_genotyper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/mem.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/mem.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/memoizing_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/memoizing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/memoizing_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/memoizing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/memusage.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/memusage.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/memusage.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/memusage.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/min_distance.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/min_distance.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/min_distance.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/min_distance.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/minimizer_mapper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/minimizer_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/minimizer_mapper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/minimizer_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/msa_converter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/msa_converter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/msa_converter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/msa_converter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_mapper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/multipath_mapper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/multipath_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/name_mapper.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/name_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/name_mapper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/name_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/nested_traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/nested_traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/nested_traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/nested_traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/null_masking_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/null_masking_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/null_masking_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/null_masking_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/option.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/option.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/option.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/option.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/packer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/packer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/packer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/packer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_component_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_component_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_component_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_component_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/path_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/path_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/phased_genome.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/phased_genome.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/phased_genome.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/phased_genome.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/pictographs.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/pictographs.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/position.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/position.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/position.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/position.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/preflight.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/preflight.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/preflight.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/preflight.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/progressive.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/progressive.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/progressive.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/progressive.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/rare_variant_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/rare_variant_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/rare_variant_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/rare_variant_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/readfilter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/region.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/region.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/region.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/region.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/region_expander.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/region_expander.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/region_expander.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/region_expander.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/reverse_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/reverse_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/reverse_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/reverse_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/sampler.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/sampler.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/sampler.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/sampler.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/scanner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/scanner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/scanner.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/scanner.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/seed_clusterer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/seed_clusterer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/seed_clusterer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/seed_clusterer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/sequence_complexity.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/sequence_complexity.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/small_bitset.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/small_bitset.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/small_snarl_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/small_snarl_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/small_snarl_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/small_snarl_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/snarl_caller.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/snarl_caller.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/snarl_caller.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/snarl_caller.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/snarls.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/snarls.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/source_sink_overlay.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/source_sink_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/source_sink_overlay.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/source_sink_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/splicing.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/splicing.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/splicing.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/splicing.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/split_strand_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/split_strand_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/split_strand_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/split_strand_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/srpe.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/srpe.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/srpe.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/srpe.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/ssw_aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/ssw_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/ssw_aligner.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/ssw_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/statistics.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/statistics.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/statistics.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/statistics.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/stream_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/stream_sorter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/stream_sorter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/stream_sorter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/stream_sorter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subgraph_overlay.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subgraph_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subgraph_overlay.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subgraph_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/surjecting_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/surjecting_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/surjecting_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/surjecting_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/surjector.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/surjector.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/surjector.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/surjector.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/swap_remove.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/swap_remove.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/transcriptome.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/transcriptome.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/transcriptome.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/transcriptome.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/translator.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/translator.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/translator.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/translator.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/traversal_support.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/traversal_support.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/traversal_support.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/traversal_support.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/tree_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/tree_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/tree_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/tree_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/types.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/utility.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/utility.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/variant_adder.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/variant_adder.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/variant_adder.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/variant_adder.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/variant_recall.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/variant_recall.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/variant_recall.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/variant_recall.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vcf_buffer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vcf_buffer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vcf_buffer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vcf_buffer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vectorizer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vectorizer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vectorizer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vectorizer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/version.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/version.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/version.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/version.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vg_set.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vg_set.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/vg_set.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/vg_set.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/viz.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/viz.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/viz.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/viz.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/wang_hash.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/wang_hash.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/watchdog.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/watchdog.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/watchdog.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/watchdog.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/a_star.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/a_star.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/alignment_path_offsets.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/approx_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/approx_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/approx_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/approx_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/dfs.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/dfs.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/dfs.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/dfs.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/disjoint_components.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/disjoint_components.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/disjoint_components.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/disjoint_components.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_head.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_head.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_head.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_head.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_tail.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_tail.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_tail.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/distance_to_tail.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/expand_context.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/expand_context.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/expand_context.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/expand_context.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_connecting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_containing_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_containing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_extending_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_extending_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/id_sort.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/id_sort.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/id_sort.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/id_sort.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/jump_along_path.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/jump_along_path.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/jump_along_path.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/jump_along_path.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/k_widest_paths.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/k_widest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/k_widest_paths.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/k_widest_paths.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/merge.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/merge.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/merge.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/merge.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/next_pos_chars.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/next_pos_chars.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/next_pos_chars.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/next_pos_chars.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/normalize.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/normalize.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/normalize.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/normalize.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/path_string.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/path_string.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/path_string.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/path_string.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/prune.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/prune.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/prune.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/prune.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/ref_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/ref_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/ref_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/ref_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/shortest_cycle.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/shortest_cycle.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/shortest_cycle.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/shortest_cycle.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/simplify_siblings.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/simplify_siblings.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/simplify_siblings.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/simplify_siblings.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/sorted_id_ranges.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/three_edge_connected_components.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/converted_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/converted_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/json_stream_helper.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/json_stream_helper.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/load_proto_to_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/load_proto_to_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/load_proto_to_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/load_proto_to_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_libvg_io.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_libvg_io.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_libvg_io.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_libvg_io.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_distance_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwt.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_gcsa.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_lcp.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_lcp.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_lcp.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_lcp.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_minimizer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_odgi.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_odgi.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_odgi.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_odgi.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_packed_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_r_index.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_r_index.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_r_index.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_r_index.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_vg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_vg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_vg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_vg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_xg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_xg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_xg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/register_loader_saver_xg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/io/save_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/io/save_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/add_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/add_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/align_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/align_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/annotate_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/annotate_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/augment_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/augment_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/autoindex_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/autoindex_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/benchmark_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/benchmark_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/call_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/call_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/chunk_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/chunk_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/circularize_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/circularize_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/cluster_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/cluster_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/combine_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/combine_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/concat_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/concat_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/construct_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/construct_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/convert_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/convert_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/deconstruct_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/deconstruct_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/depth_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/depth_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/dotplot_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/dotplot_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/explode_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/explode_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/filter_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/filter_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/find_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/find_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gamcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gamcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gampcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gampcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gamsort_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gamsort_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gbwt_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/gbwt_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/genotype_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/genotype_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/giraffe_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/giraffe_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/help_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/help_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/ids_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/ids_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/index_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/index_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/inject_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/inject_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/join_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/join_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/kmers_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/kmers_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/map_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/map_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mcmc_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mcmc_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/minimizer_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/minimizer_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mod_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mod_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mpmap_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/mpmap_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/msga_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/msga_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/pack_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/pack_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/paths_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/paths_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/prune_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/prune_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/recalibrate_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/recalibrate_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/rna_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/rna_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sift_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sift_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sim_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sim_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/simplify_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/simplify_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/snarls_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/snarls_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sort_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/sort_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/srpe_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/srpe_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/stats_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/stats_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/surject_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/surject_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/test_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/test_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/trace_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/trace_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/translate_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/translate_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/validate_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/validate_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/vectorize_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/vectorize_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/version_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/version_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/view_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/view_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/subcommand/viz_main.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/viz_main.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/unittest/driver.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/unittest/driver.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/src/unittest/driver.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/src/unittest/driver.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/bin2ascii.h... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/bin2ascii.h... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/edit.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/edit.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/edit.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/json2pb.h... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/json2pb.h... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/loader.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/loader.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/vpkg.hpp... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgi/build/reproducible-path/vg-1.30.0+ds/src/qual_adj_xdrop_aligner.cpp:2: warning: the name 'qual_adj_xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/src/xdrop_aligner.cpp:2: warning: the name 'xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_containing_graph.hpp:5: warning: the name 'extract_containing_graphs.hpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/extract_extending_graph.hpp:5: warning: the name 'extract_extending_graphs.hpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp:5: warning: the name 'handle_graphs.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp:5: warning: the name 'stream_multiplexer.chpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.30.0+ds/src/alignment.hpp:281: warning: no matching file member found for void vg::parse_bed_regions(istream &bedstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments) Possible candidates: 'void parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 1773 of file /build/reproducible-path/vg-1.30.0+ds/src/alignment.cpp 'void parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)' at line 28 of file /build/reproducible-path/vg-1.30.0+ds/src/region.cpp /build/reproducible-path/vg-1.30.0+ds/src/alignment.hpp:282: warning: no matching file member found for void vg::parse_gff_regions(istream >fstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments) Possible candidates: 'void parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 1856 of file /build/reproducible-path/vg-1.30.0+ds/src/alignment.cpp /build/reproducible-path/vg-1.30.0+ds/src/benchmark.hpp:48: warning: no matching file member found for ostream & vg::operator<<(ostream &out, const vg::BenchmarkResult &result) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/cluster.hpp:769: warning: no matching file member found for bdsg::HashGraph vg::cluster_subgraph_containing(const handlegraph::HandleGraph &base, const vg::Alignment &aln, const vector< vg::vg::MaximalExactMatch > &cluster, const vg::GSSWAligner *aligner) Possible candidates: 'bdsg::HashGraph cluster_subgraph_containing(const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &cluster, const GSSWAligner *aligner)' at line 3827 of file /build/reproducible-path/vg-1.30.0+ds/src/cluster.cpp /build/reproducible-path/vg-1.30.0+ds/src/cluster.hpp:772: warning: no matching file member found for bdsg::HashGraph vg::cluster_subgraph_walk(const handlegraph::HandleGraph &base, const vg::Alignment &aln, const vector< vg::vg::MaximalExactMatch > &mems, double expansion) Possible candidates: 'bdsg::HashGraph cluster_subgraph_walk(const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &mems, double expansion)' at line 3848 of file /build/reproducible-path/vg-1.30.0+ds/src/cluster.cpp /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.hpp:504: warning: no matching file member found for ostream & vg::operator<<(ostream &stream, const vg::Support &support) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/gfa.hpp:21: warning: no matching file member found for void vg::graph_to_gfa(const unique_ptr< handlegraph::PathHandleGraph > &graph, ostream &out) Possible candidates: 'void graph_to_gfa(const unique_ptr< PathHandleGraph > &graph, ostream &out)' at line 9 of file /build/reproducible-path/vg-1.30.0+ds/src/gfa.cpp /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.hpp:47: warning: no matching file member found for void vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< vector< gbwt::node_type >, int >> &haplotype_list, const handlegraph::HandleGraph &source, bool json=true) Possible candidates: 'Graph output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)' at line 71 of file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.cpp 'void output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)' at line 88 of file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.cpp /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.hpp:54: warning: no matching file member found for void vg::output_haplotype_counts(ostream &annotation_ostream, vector< pair< vector< gbwt::node_type >, int >> &haplotype_list) Possible candidates: 'void output_haplotype_counts(ostream &annotation_ostream, vector< pair< thread_t, int >> &haplotype_list)' at line 64 of file /build/reproducible-path/vg-1.30.0+ds/src/haplotype_extracter.cpp /build/reproducible-path/vg-1.30.0+ds/src/kmer.hpp:49: warning: no matching file member found for ostream & vg::operator<<(ostream &out, const vg::kmer_t &kmer) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/kmer.hpp:62: warning: no matching file member found for void vg::write_gcsa_kmers(const handlegraph::HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, long long int head_id, long long int tail_id) Possible candidates: 'void write_gcsa_kmers(const HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, id_t head_id, id_t tail_id)' at line 227 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.hpp:379: warning: no matching file member found for void vg::view_multipath_alignment(ostream &out, const vg::multipath_alignment_t &multipath_aln, const handlegraph::HandleGraph &handle_graph) Possible candidates: 'void view_multipath_alignment(ostream &out, const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph)' at line 3889 of file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.cpp /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.hpp:382: warning: no matching file member found for void vg::view_multipath_alignment_as_dot(ostream &out, const vg::multipath_alignment_t &multipath_aln, bool show_graph=false) Possible candidates: 'void view_multipath_alignment_as_dot(ostream &out, const multipath_alignment_t &multipath_aln, bool show_graph)' at line 3994 of file /build/reproducible-path/vg-1.30.0+ds/src/multipath_alignment.cpp /build/reproducible-path/vg-1.30.0+ds/src/path.hpp:40: warning: no matching file member found for ostream & vg::operator<<(ostream &out, vg::mapping_t mapping) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/readfilter.hpp:292: warning: no matching file member found for ostream & vg::operator<<(ostream &os, const vg::Counts &counts) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/snarls.hpp:806: warning: no matching file member found for ostream & vg::operator<<(ostream &out, const vg::Visit &visit) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/snarls.hpp:846: warning: no matching file member found for ostream & vg::operator<<(ostream &out, const vg::Snarl &snarl) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/stream_index.hpp:99: warning: no matching file member found for ostream & vg::operator<<(ostream &out, const vg::BitString &bs) Possible candidates: 'ostream & operator<<(ostream &out, const BenchmarkResult &result)' at line 45 of file /build/reproducible-path/vg-1.30.0+ds/src/benchmark.cpp 'ostream & operator<<(ostream &stream, const Support &support)' at line 659 of file /build/reproducible-path/vg-1.30.0+ds/src/genotypekit.cpp 'ostream & operator<<(ostream &out, const kmer_t &kmer)' at line 178 of file /build/reproducible-path/vg-1.30.0+ds/src/kmer.cpp 'ostream & operator<<(ostream &out, const MaximalExactMatch &mem)' at line 49 of file /build/reproducible-path/vg-1.30.0+ds/src/mem.cpp 'ostream & operator<<(ostream &out, const NodeSide &nodeside)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/src/nodeside.hpp 'ostream & operator<<(ostream &out, const NodeTraversal &nodetraversal)' at line 73 of file /build/reproducible-path/vg-1.30.0+ds/src/nodetraversal.hpp 'ostream & operator<<(ostream &out, mapping_t mapping)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/path.cpp 'std::ostream & operator<<(std::ostream &out, PathBranch branch)' at line 106 of file /build/reproducible-path/vg-1.30.0+ds/src/phase_unfolder.cpp 'ostream & operator<<(ostream &os, const Counts &counts)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/readfilter.cpp 'ostream & operator<<(ostream &out, const Visit &visit)' at line 2402 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'ostream & operator<<(ostream &out, const Snarl &snarl)' at line 2480 of file /build/reproducible-path/vg-1.30.0+ds/src/snarls.cpp 'auto operator<<(ostream &out, const BitString &bs) -> ostream &' at line 130 of file /build/reproducible-path/vg-1.30.0+ds/src/stream_index.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 93 of file /build/reproducible-path/vg-1.30.0+ds/src/types.hpp 'std::ostream & operator<<(std::ostream &out, const kmer_t &kmer)' at line 102 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/kmer.cpp 'std::ostream & operator<<(std::ostream &out, const walk_t &walk)' at line 107 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/walk.cpp 'std::ostream & operator<<(std::ostream &out, const CommandCategory &category)' at line 13 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/subcommand.cpp 'std::ostream & operator<<(std::ostream &out, const pos_t &pos)' at line 103 of file /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/xg.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)' at line 224 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp 'std::ostream & operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)' at line 238 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp /build/reproducible-path/vg-1.30.0+ds/src/utility.hpp:69: warning: no matching file member found for void vg::write_fasta_sequence(const std::string &name, const std::string &sequence, ostream &os, size_t width=80) Possible candidates: 'void write_fasta_sequence(const std::string &name, const std::string &sequence, ostream &os, size_t width)' at line 273 of file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp /build/reproducible-path/vg-1.30.0+ds/src/utility.hpp:423: warning: no matching file member found for void vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback) Possible candidates: 'void get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)' at line 446 of file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp 'void get_input_file(const string &file_name, function< void(istream &)> callback)' at line 491 of file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp /build/reproducible-path/vg-1.30.0+ds/src/utility.hpp:436: warning: no matching file member found for void vg::get_input_file(const string &file_name, function< void(istream &)> callback) Possible candidates: 'void get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)' at line 446 of file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp 'void get_input_file(const string &file_name, function< void(istream &)> callback)' at line 491 of file /build/reproducible-path/vg-1.30.0+ds/src/utility.cpp /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.hpp:22: warning: no matching file member found for void vg::algorithms::packed_depths(const vg::Packer &packer, const string &path_name, size_t min_coverage, ostream &out_stream) Possible candidates: 'void packed_depths(const Packer &packer, const string &path_name, size_t min_coverage, ostream &out_stream)' at line 10 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/coverage_depth.cpp /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.hpp:50: warning: no matching file member found for void vg::algorithms::gfa_to_path_handle_graph_in_memory(istream &in, handlegraph::MutablePathMutableHandleGraph *graph) Possible candidates: 'void gfa_to_path_handle_graph_in_memory(istream &in, MutablePathMutableHandleGraph *graph)' at line 246 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/gfa_to_handle.cpp /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.hpp:13: warning: no matching file member found for void vg::algorithms::to_gfa(const handlegraph::PathHandleGraph &graph, ostream &out) Possible candidates: 'void to_gfa(const PathHandleGraph &graph, ostream &out)' at line 8 of file /build/reproducible-path/vg-1.30.0+ds/src/algorithms/to_gfa.cpp /build/reproducible-path/vg-1.30.0+ds/src/subcommand/chunk_main.cpp:853: warning: no matching file member found for int split_gam(istream &gam_stream, size_t chunk_size, const string &out_prefix, size_t gam_buffer_size) Possible candidates: 'static int split_gam(istream &gam_stream, size_t chunk_size, const string &out_prefix, size_t gam_buffer_size=100)' at line 853 of file /build/reproducible-path/vg-1.30.0+ds/src/subcommand/chunk_main.cpp /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:64: warning: no matching file member found for load_function_t vg::io::wrap_bare_loader(function< void *(istream &)> istream_loader) Possible candidates: 'auto wrap_bare_loader(function< void *(istream &)> istream_loader) -> load_function_t' at line 105 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:70: warning: no matching file member found for void vg::io::with_function_calling_stream(const function< void(const string &)> &emit_message, const function< void(ostream &)> &use_stream) Possible candidates: 'void with_function_calling_stream(const message_consumer_function_t &emit_message, const function< void(ostream &)> &use_stream)' at line 197 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/registry.hpp:76: warning: no matching file member found for save_function_t vg::io::wrap_bare_saver(const function< void(void *, ostream &)> ostream_saver) Possible candidates: 'auto wrap_bare_saver(function< void(const void *, ostream &)> ostream_saver) -> save_function_t' at line 312 of file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/registry.cpp o/include/vg/io/vpkg.hpp... Preprocessing /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto... Parsing file /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating file documentation... Generating docs for file deps/libhandlegraph/src/append_graph.cpp... Generating docs for file deps/libhandlegraph/src/apply_orientations.cpp... Generating docs for file deps/libhandlegraph/src/are_equivalent.cpp... Generating docs for file deps/libhandlegraph/src/copy_graph.cpp... Generating docs for file deps/libhandlegraph/src/count_walks.cpp... Generating docs for file deps/libhandlegraph/src/dagify.cpp... Generating docs for file deps/libhandlegraph/src/deletable_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/dijkstra.cpp... Generating docs for file deps/libhandlegraph/src/eades_algorithm.cpp... Generating docs for file deps/libhandlegraph/src/extend.cpp... Generating docs for file deps/libhandlegraph/src/find_shortest_paths.cpp... Generating docs for file deps/libhandlegraph/src/find_tips.cpp... Generating docs for file deps/libhandlegraph/src/handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/util.hpp... Generating docs for file deps/libhandlegraph/src/is_acyclic.cpp... Generating docs for file deps/libhandlegraph/src/is_single_stranded.cpp... Generating docs for file deps/libhandlegraph/src/mutable_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/path_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/path_position_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/ranked_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/reverse_complement.cpp... Generating docs for file deps/libhandlegraph/src/serializable.cpp... Generating docs for file deps/libhandlegraph/src/snarl_decomposition.cpp... Generating docs for file deps/libhandlegraph/src/split_strands.cpp... Generating docs for file deps/libhandlegraph/src/strongly_connected_components.cpp... Generating docs for file deps/libhandlegraph/src/topological_sort.cpp... Generating docs for file deps/libhandlegraph/src/trivially_serializable.cpp... Generating docs for file deps/libhandlegraph/src/types.cpp... Generating docs for file deps/libhandlegraph/src/unchop.cpp... Generating docs for file deps/libhandlegraph/src/weakly_connected_components.cpp... Generating docs for file deps/libvgio/deps/vg.proto... Generating docs for file deps/libvgio/include/vg/io/alignment_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/alignment_io.hpp... Generating docs for file deps/libvgio/include/vg/io/basic_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/edit.hpp... Generating docs for file deps/libvgio/include/vg/io/fdstream.hpp... Generating docs for file deps/libvgio/include/vg/io/gafkluge.hpp... Generating docs for file deps/libvgio/include/vg/io/hfile_cppstream.hpp... Generating docs for file deps/libvgio/include/vg/io/hfile_internal.hpp... Generating docs for file deps/libvgio/include/vg/io/json2pb.h... Generating docs for file deps/libvgio/include/vg/io/loader.hpp... Generating docs for file deps/libvgio/include/vg/io/message_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/message_iterator.hpp... Generating docs for file deps/libvgio/include/vg/io/protobuf_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/protobuf_iterator.hpp... Generating docs for file deps/libvgio/include/vg/io/registry.hpp... Generating docs for file deps/libvgio/include/vg/io/stream.hpp... Generating docs for file deps/libvgio/include/vg/io/stream_multiplexer.hpp... Generating docs for file deps/libvgio/include/vg/io/vpkg.hpp... Generating docs for file deps/libvgio/src/alignment_emitter.cpp... Generating docs for file deps/libvgio/src/alignment_io.cpp... Generating docs for file deps/libvgio/src/basic_stream.cpp... Generating docs for file deps/libvgio/src/bin2ascii.h... Generating docs for file deps/libvgio/src/blocked_gzip_input_stream.cpp... Generating docs for file deps/libvgio/src/blocked_gzip_output_stream.cpp... Generating docs for file deps/libvgio/src/edit.cpp... Generating docs for file deps/libvgio/src/hfile_cppstream.cpp... Generating docs for file deps/libvgio/src/json2pb.cpp... Generating docs for file deps/libvgio/src/message_emitter.cpp... Generating docs for file deps/libvgio/src/message_iterator.cpp... Generating docs for file deps/libvgio/src/registry.cpp... Generating docs for file deps/libvgio/src/stream.cpp... Generating docs for file deps/libvgio/src/stream_multiplexer.cpp... Generating docs for file deps/libvgio/src/vpkg.cpp... Generating docs for file deps/xg/src/xg.cpp... Generating docs for file deps/xg/src/xg.hpp... Generating docs for file src/algorithms/a_star.hpp... Generating docs for file src/algorithms/alignment_path_offsets.cpp... Generating docs for file src/algorithms/alignment_path_offsets.hpp... Generating docs for file src/algorithms/approx_path_distance.cpp... Generating docs for file src/algorithms/approx_path_distance.hpp... Generating docs for file src/algorithms/coverage_depth.cpp... Generating docs for file src/algorithms/coverage_depth.hpp... Generating docs for file src/algorithms/dfs.cpp... Generating docs for file src/algorithms/dfs.hpp... Generating docs for file src/algorithms/disjoint_components.cpp... Generating docs for file src/algorithms/disjoint_components.hpp... Generating docs for file src/algorithms/distance_to_head.cpp... Generating docs for file src/algorithms/distance_to_head.hpp... Generating docs for file src/algorithms/distance_to_tail.cpp... Generating docs for file src/algorithms/distance_to_tail.hpp... Generating docs for file src/algorithms/expand_context.cpp... Generating docs for file src/algorithms/expand_context.hpp... Generating docs for file src/algorithms/extract_connecting_graph.cpp... Generating docs for file src/algorithms/extract_connecting_graph.hpp... Generating docs for file src/algorithms/extract_containing_graph.cpp... Generating docs for file src/algorithms/extract_containing_graph.hpp... Generating docs for file src/algorithms/extract_extending_graph.cpp... Generating docs for file src/algorithms/extract_extending_graph.hpp... Generating docs for file src/algorithms/gfa_to_handle.cpp... Generating docs for file src/algorithms/gfa_to_handle.hpp... Generating docs for file src/algorithms/id_sort.cpp... Generating docs for file src/algorithms/id_sort.hpp... Generating docs for file src/algorithms/jump_along_path.cpp... Generating docs for file src/algorithms/jump_along_path.hpp... Generating docs for file src/algorithms/k_widest_paths.cpp... Generating docs for file src/algorithms/k_widest_paths.hpp... Generating docs for file src/algorithms/merge.cpp... Generating docs for file src/algorithms/merge.hpp... Generating docs for file src/algorithms/nearest_offsets_in_paths.cpp... Generating docs for file src/algorithms/nearest_offsets_in_paths.hpp... Generating docs for file src/algorithms/next_pos_chars.cpp... Generating docs for file src/algorithms/next_pos_chars.hpp... Generating docs for file src/algorithms/normalize.cpp... Generating docs for file src/algorithms/normalize.hpp... Generating docs for file src/algorithms/path_string.cpp... Generating docs for file src/algorithms/path_string.hpp... Generating docs for file src/algorithms/prune.cpp... Generating docs for file src/algorithms/prune.hpp... Generating docs for file src/algorithms/ref_path_distance.cpp... Generating docs for file src/algorithms/ref_path_distance.hpp... Generating docs for file src/algorithms/shortest_cycle.cpp... Generating docs for file src/algorithms/shortest_cycle.hpp... Generating docs for file src/algorithms/simplify_siblings.cpp... Generating docs for file src/algorithms/simplify_siblings.hpp... Generating docs for file src/algorithms/sorted_id_ranges.cpp... Generating docs for file src/algorithms/sorted_id_ranges.hpp... Generating docs for file src/algorithms/three_edge_connected_components.cpp... Generating docs for file src/algorithms/three_edge_connected_components.hpp... Generating docs for file src/algorithms/to_gfa.cpp... Generating docs for file src/algorithms/to_gfa.hpp... Generating docs for file src/algorithms/walk.cpp... Generating docs for file src/algorithms/walk.hpp... Generating docs for file src/aligner.cpp... Generating docs for file src/aligner.hpp... Generating docs for file src/alignment.cpp... Generating docs for file src/alignment.hpp... Generating docs for file src/annotation.hpp... Generating docs for file src/augment.cpp... Generating docs for file src/augment.hpp... Generating docs for file src/banded_global_aligner.cpp... Generating docs for file src/banded_global_aligner.hpp... Generating docs for file src/benchmark.cpp... Generating docs for file src/benchmark.hpp... Generating docs for file src/build_index.cpp... Generating docs for file src/build_index.hpp... Generating docs for file src/cactus.cpp... Generating docs for file src/cactus.hpp... Generating docs for file src/cactus_snarl_finder.cpp... Generating docs for file src/cactus_snarl_finder.hpp... Generating docs for file src/chunker.cpp... Generating docs for file src/chunker.hpp... Generating docs for file src/cluster.cpp... Generating docs for file src/cluster.hpp... Generating docs for file src/colors.hpp... Generating docs for file src/constructor.cpp... Generating docs for file src/constructor.hpp... Generating docs for file src/convert.hpp... Generating docs for file src/crash.cpp... Generating docs for file src/crash.hpp... Generating docs for file src/dagified_graph.cpp... Generating docs for file src/dagified_graph.hpp... Generating docs for file src/deconstructor.cpp... Generating docs for file src/deconstructor.hpp... Generating docs for file src/deletion_aligner.cpp... Generating docs for file src/deletion_aligner.hpp... Generating docs for file src/dinucleotide_machine.cpp... Generating docs for file src/dinucleotide_machine.hpp... Generating docs for file src/dozeu_interface.cpp... Generating docs for file src/dozeu_interface.hpp... Generating docs for file src/dozeu_pinning_overlay.cpp... Generating docs for file src/dozeu_pinning_overlay.hpp... Generating docs for file src/endianness.hpp... Generating docs for file src/entropy.cpp... Generating docs for file src/entropy.hpp... Generating docs for file src/extra_node_graph.cpp... Generating docs for file src/extra_node_graph.hpp... Generating docs for file src/feature_set.cpp... Generating docs for file src/feature_set.hpp... Generating docs for file src/filter.cpp... Generating docs for file src/filter.hpp... Generating docs for file src/flow_sort.cpp... Generating docs for file src/flow_sort.hpp... Generating docs for file src/funnel.cpp... Generating docs for file src/funnel.hpp... Generating docs for file src/gapless_extender.cpp... Generating docs for file src/gapless_extender.hpp... Generating docs for file src/gbwt_helper.cpp... Generating docs for file src/gbwt_helper.hpp... Generating docs for file src/genome_state.cpp... Generating docs for file src/genome_state.hpp... Generating docs for file src/genotypekit.cpp... Generating docs for file src/genotypekit.hpp... Generating docs for file src/genotyper.cpp... Generating docs for file src/genotyper.hpp... Generating docs for file src/gfa.cpp... Generating docs for file src/gfa.hpp... Generating docs for file src/gff_reader.cpp... Generating docs for file src/gff_reader.hpp... Generating docs for file src/graph.cpp... Generating docs for file src/graph.hpp... Generating docs for file src/graph_caller.cpp... Generating docs for file src/graph_caller.hpp... Generating docs for file src/graph_synchronizer.cpp... Generating docs for file src/graph_synchronizer.hpp... Generating docs for file src/handle.hpp... Generating docs for file src/haplotype_extracter.cpp... Generating docs for file src/haplotype_extracter.hpp... Generating docs for file src/haplotype_indexer.cpp... Generating docs for file src/haplotype_indexer.hpp... Generating docs for file src/haplotypes.cpp... Generating docs for file src/haplotypes.hpp... Generating docs for file src/hash_map.hpp... Generating docs for file src/homogenizer.cpp... Generating docs for file src/homogenizer.hpp... Generating docs for file src/hts_alignment_emitter.cpp... Generating docs for file src/hts_alignment_emitter.hpp... Generating docs for file src/identity_overlay.cpp... Generating docs for file src/identity_overlay.hpp... Generating docs for file src/incremental_subgraph.cpp... Generating docs for file src/incremental_subgraph.hpp... Generating docs for file src/index_manager.cpp... Generating docs for file src/index_manager.hpp... Generating docs for file src/index_registry.cpp... Generating docs for file src/index_registry.hpp... Generating docs for file src/indexed_vg.cpp... Generating docs for file src/indexed_vg.hpp... Generating docs for file src/integrated_snarl_finder.cpp... Generating docs for file src/integrated_snarl_finder.hpp... Generating docs for file src/io/converted_hash_graph.hpp... Generating docs for file src/io/json_stream_helper.hpp... Generating docs for file src/io/load_proto_to_graph.cpp... Generating docs for file src/io/load_proto_to_graph.hpp... Generating docs for file src/io/register_libvg_io.cpp... Generating docs for file src/io/register_libvg_io.hpp... Generating docs for file src/io/register_loader_saver_distance_index.cpp... Generating docs for file src/io/register_loader_saver_distance_index.hpp... Generating docs for file src/io/register_loader_saver_gbwt.cpp... Generating docs for file src/io/register_loader_saver_gbwt.hpp... Generating docs for file src/io/register_loader_saver_gbwtgraph.cpp... Generating docs for file src/io/register_loader_saver_gbwtgraph.hpp... Generating docs for file src/io/register_loader_saver_gcsa.cpp... Generating docs for file src/io/register_loader_saver_gcsa.hpp... Generating docs for file src/io/register_loader_saver_hash_graph.cpp... Generating docs for file src/io/register_loader_saver_hash_graph.hpp... Generating docs for file src/io/register_loader_saver_lcp.cpp... Generating docs for file src/io/register_loader_saver_lcp.hpp... Generating docs for file src/io/register_loader_saver_minimizer.cpp... Generating docs for file src/io/register_loader_saver_minimizer.hpp... Generating docs for file src/io/register_loader_saver_odgi.cpp... Generating docs for file src/io/register_loader_saver_odgi.hpp... Generating docs for file src/io/register_loader_saver_packed_graph.cpp... Generating docs for file src/io/register_loader_saver_packed_graph.hpp... Generating docs for file src/io/register_loader_saver_r_index.cpp... Generating docs for file src/io/register_loader_saver_r_index.hpp... Generating docs for file src/io/register_loader_saver_snarl_manager.cpp... Generating docs for file src/io/register_loader_saver_snarl_manager.hpp... Generating docs for file src/io/register_loader_saver_vg.cpp... Generating docs for file src/io/register_loader_saver_vg.hpp... Generating docs for file src/io/register_loader_saver_xg.cpp... Generating docs for file src/io/register_loader_saver_xg.hpp... Generating docs for file src/io/save_handle_graph.hpp... Generating docs for file src/kmer.cpp... Generating docs for file src/algorithms/kmer.cpp... Generating docs for file src/kmer.hpp... Generating docs for file src/algorithms/kmer.hpp... Generating docs for file src/main.cpp... Generating docs for file src/mapper.cpp... Generating docs for file src/mapper.hpp... Generating docs for file src/mcmc_caller.cpp... Generating docs for file src/mcmc_caller.hpp... Generating docs for file src/mcmc_genotyper.cpp... Generating docs for file src/mcmc_genotyper.hpp... Generating docs for file src/mem.cpp... Generating docs for file src/mem.hpp... Generating docs for file src/memoizing_graph.cpp... Generating docs for file src/memoizing_graph.hpp... Generating docs for file src/memusage.cpp... Generating docs for file src/memusage.hpp... Generating docs for file src/min_distance.cpp... Generating docs for file src/min_distance.hpp... Generating docs for file src/minimizer_mapper.cpp... Generating docs for file src/minimizer_mapper.hpp... Generating docs for file src/msa_converter.cpp... Generating docs for file src/msa_converter.hpp... Generating docs for file src/multipath_alignment.cpp... Generating docs for file src/multipath_alignment.hpp... Generating docs for file src/multipath_alignment_emitter.cpp... Generating docs for file src/multipath_alignment_emitter.hpp... Generating docs for file src/multipath_alignment_graph.cpp... Generating docs for file src/multipath_alignment_graph.hpp... Generating docs for file src/multipath_mapper.cpp... Generating docs for file src/multipath_mapper.hpp... Generating docs for file src/name_mapper.cpp... Generating docs for file src/name_mapper.hpp... Generating docs for file src/nested_traversal_finder.cpp... Generating docs for file src/nested_traversal_finder.hpp... Generating docs for file src/nodeside.hpp... Generating docs for file src/nodetraversal.hpp... Generating docs for file src/null_masking_graph.cpp... Generating docs for file src/null_masking_graph.hpp... Generating docs for file src/option.cpp... Generating docs for file src/option.hpp... Generating docs for file src/packer.cpp... Generating docs for file src/packer.hpp... Generating docs for file src/path.cpp... Generating docs for file src/path.hpp... Generating docs for file src/path_component_index.cpp... Generating docs for file src/path_component_index.hpp... Generating docs for file src/path_index.cpp... Generating docs for file src/path_index.hpp... Generating docs for file src/path_subgraph.cpp... Generating docs for file src/path_subgraph.hpp... Generating docs for file src/phase_unfolder.cpp... Generating docs for file src/phase_unfolder.hpp... Generating docs for file src/phased_genome.cpp... Generating docs for file src/phased_genome.hpp... Generating docs for file src/pictographs.hpp... Generating docs for file src/position.cpp... Generating docs for file src/position.hpp... Generating docs for file src/preflight.cpp... Generating docs for file src/preflight.hpp... Generating docs for file src/progressive.cpp... Generating docs for file src/progressive.hpp... Generating docs for file src/qual_adj_xdrop_aligner.cpp... Generating docs for file src/rare_variant_simplifier.cpp... Generating docs for file src/rare_variant_simplifier.hpp... Generating docs for file src/readfilter.cpp... Generating docs for file src/readfilter.hpp... Generating docs for file src/region.cpp... Generating docs for file src/region.hpp... Generating docs for file src/region_expander.cpp... Generating docs for file src/region_expander.hpp... Generating docs for file src/reverse_graph.cpp... Generating docs for file src/reverse_graph.hpp... Generating docs for file src/sampler.cpp... Generating docs for file src/sampler.hpp... Generating docs for file src/scanner.cpp... Generating docs for file src/scanner.hpp... Generating docs for file src/seed_clusterer.cpp... Generating docs for file src/seed_clusterer.hpp... Generating docs for file src/sequence_complexity.hpp... Generating docs for file src/small_bitset.hpp... Generating docs for file src/small_snarl_simplifier.cpp... Generating docs for file src/small_snarl_simplifier.hpp... Generating docs for file src/snarl_caller.cpp... Generating docs for file src/snarl_caller.hpp... Generating docs for file src/snarls.cpp... Generating docs for file src/snarls.hpp... Generating docs for file src/source_sink_overlay.cpp... Generating docs for file src/source_sink_overlay.hpp... Generating docs for file src/splicing.cpp... Generating docs for file src/splicing.hpp... Generating docs for file src/split_strand_graph.cpp... Generating docs for file src/split_strand_graph.hpp... Generating docs for file src/srpe.cpp... Generating docs for file src/srpe.hpp... Generating docs for file src/ssw_aligner.cpp... Generating docs for file src/ssw_aligner.hpp... Generating docs for file src/statistics.cpp... Generating docs for file src/statistics.hpp... Generating docs for file src/stream_index.cpp... Generating docs for file src/stream_index.hpp... Generating docs for file src/stream_sorter.cpp... Generating docs for file src/stream_sorter.hpp... Generating docs for file src/subcommand/add_main.cpp... Generating docs for file src/subcommand/align_main.cpp... Generating docs for file src/subcommand/annotate_main.cpp... Generating docs for file src/subcommand/augment_main.cpp... Generating docs for file src/subcommand/autoindex_main.cpp... Generating docs for file src/subcommand/benchmark_main.cpp... Generating docs for file src/subcommand/call_main.cpp... Generating docs for file src/subcommand/chunk_main.cpp... Generating docs for file src/subcommand/circularize_main.cpp... Generating docs for file src/subcommand/cluster_main.cpp... Generating docs for file src/subcommand/combine_main.cpp... Generating docs for file src/subcommand/concat_main.cpp... Generating docs for file src/subcommand/construct_main.cpp... Generating docs for file src/subcommand/convert_main.cpp... Generating docs for file src/subcommand/deconstruct_main.cpp... Generating docs for file src/subcommand/depth_main.cpp... Generating docs for file src/subcommand/dotplot_main.cpp... Generating docs for file src/subcommand/explode_main.cpp... Generating docs for file src/subcommand/filter_main.cpp... Generating docs for file src/subcommand/find_main.cpp... Generating docs for file src/subcommand/gamcompare_main.cpp... Generating docs for file src/subcommand/gampcompare_main.cpp... Generating docs for file src/subcommand/gamsort_main.cpp... Generating docs for file src/subcommand/gbwt_main.cpp... Generating docs for file src/subcommand/genotype_main.cpp... Generating docs for file src/subcommand/giraffe_main.cpp... Generating docs for file src/subcommand/help_main.cpp... Generating docs for file src/subcommand/ids_main.cpp... Generating docs for file src/subcommand/index_main.cpp... Generating docs for file src/subcommand/inject_main.cpp... Generating docs for file src/subcommand/join_main.cpp... Generating docs for file src/subcommand/kmers_main.cpp... Generating docs for file src/subcommand/map_main.cpp... Generating docs for file src/subcommand/mcmc_main.cpp... Generating docs for file src/subcommand/minimizer_main.cpp... Generating docs for file src/subcommand/mod_main.cpp... Generating docs for file src/subcommand/mpmap_main.cpp... Generating docs for file src/subcommand/msga_main.cpp... Generating docs for file src/subcommand/pack_main.cpp... Generating docs for file src/subcommand/paths_main.cpp... Generating docs for file src/subcommand/prune_main.cpp... Generating docs for file src/subcommand/recalibrate_main.cpp... Generating docs for file src/subcommand/rna_main.cpp... Generating docs for file src/subcommand/sift_main.cpp... Generating docs for file src/subcommand/sim_main.cpp... Generating docs for file src/subcommand/simplify_main.cpp... Generating docs for file src/subcommand/snarls_main.cpp... Generating docs for file src/subcommand/sort_main.cpp... Generating docs for file src/subcommand/srpe_main.cpp... Generating docs for file src/subcommand/stats_main.cpp... Generating docs for file src/subcommand/subcommand.cpp... Generating docs for file src/subcommand/subcommand.hpp... Generating docs for file src/subcommand/surject_main.cpp... Generating docs for file src/subcommand/test_main.cpp... Generating docs for file src/subcommand/trace_main.cpp... Generating docs for file src/subcommand/translate_main.cpp... Generating docs for file src/subcommand/validate_main.cpp... Generating docs for file src/subcommand/vectorize_main.cpp... Generating docs for file src/subcommand/version_main.cpp... Generating docs for file src/subcommand/view_main.cpp... Generating docs for file src/subcommand/viz_main.cpp... Generating docs for file src/subgraph.cpp... Generating docs for file src/algorithms/subgraph.cpp... Generating docs for file src/subgraph.hpp... Generating docs for file src/algorithms/subgraph.hpp... Generating docs for file src/subgraph_overlay.cpp... Generating docs for file src/subgraph_overlay.hpp... Generating docs for file src/surjecting_alignment_emitter.cpp... Generating docs for file src/surjecting_alignment_emitter.hpp... Generating docs for file src/surjector.cpp... Generating docs for file src/surjector.hpp... Generating docs for file src/swap_remove.hpp... Generating docs for file src/transcriptome.cpp... Generating docs for file src/transcriptome.hpp... Generating docs for file src/translator.cpp... Generating docs for file src/translator.hpp... Generating docs for file src/traversal_finder.cpp... Generating docs for file src/traversal_finder.hpp... Generating docs for file src/traversal_support.cpp... Generating docs for file src/traversal_support.hpp... Generating docs for file src/tree_subgraph.cpp... Generating docs for file src/tree_subgraph.hpp... Generating docs for file src/types.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/types.hpp... Generating docs for file src/unittest/driver.cpp... Generating docs for file src/unittest/driver.hpp... Generating docs for file src/utility.cpp... Generating docs for file src/utility.hpp... Generating docs for file src/variant_adder.cpp... Generating docs for file src/variant_adder.hpp... Generating docs for file src/variant_recall.cpp... Generating docs for file src/variant_recall.hpp... Generating docs for file src/vcf_buffer.cpp... Generating docs for file src/vcf_buffer.hpp... Generating docs for file src/vectorizer.cpp... Generating docs for file src/vectorizer.hpp... Generating docs for file src/version.cpp... Generating docs for file src/version.hpp... Generating docs for file src/vg.cpp... Generating docs for file src/vg.hpp... Generating docs for file src/vg_set.cpp... Generating docs for file src/vg_set.hpp... Generating docs for file src/viz.cpp... Generating docs for file src/viz.hpp... Generating docs for file src/wang_hash.hpp... Generating docs for file src/watchdog.cpp... Generating docs for file src/watchdog.hpp... Generating docs for file src/xdrop_aligner.cpp... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound hFILE_backend... Generating docs for compound j2pb_error... Generating docs for compound job_type... Generating docs for compound json_autoptr... Generating docs for compound PruningParameters... Generating docs for compound Vectorizer... Generating namespace index... Generating docs for namespace gafkluge Generating docs for compound gafkluge::GafStep... Generating docs for compound gafkluge::GafRecord... Generating docs for namespace google Generating docs for namespace google::protobuf Generating docs for namespace handlegraph Generating docs for compound handlegraph::BuildableSnarlDecomposition... Generating docs for compound handlegraph::DeletableHandleGraph... Generating docs for compound handlegraph::ExpandingOverlayGraph... Generating docs for compound handlegraph::HandleGraph... Generating docs for compound handlegraph::RankedHandleGraph... Generating docs for compound handlegraph::VectorizableHandleGraph... Generating docs for compound handlegraph::BoolReturningWrapper... Generating docs for compound handlegraph::BoolReturningWrapper< Iteratee, Iterated, void >... Generating docs for compound handlegraph::BoolReturningWrapper< Iteratee, Iterated, bool >... Generating docs for compound handlegraph::MutableHandleGraph... Generating docs for compound handlegraph::MutablePathDeletableHandleGraph... Generating docs for compound handlegraph::MutablePathHandleGraph... Generating docs for compound handlegraph::MutablePathMutableHandleGraph... Generating docs for compound handlegraph::PathHandleGraph... Generating docs for compound handlegraph::PathForEachSocket... Generating docs for nested compound handlegraph::PathForEachSocket::iterator... Generating docs for compound handlegraph::PathPositionHandleGraph... Generating docs for compound handlegraph::Serializable... Generating docs for compound handlegraph::SerializableHandleGraph... Generating docs for compound handlegraph::SnarlDecomposition... Generating docs for compound handlegraph::TriviallySerializable... Generating docs for compound handlegraph::handle_t... Generating docs for compound handlegraph::path_handle_t... Generating docs for compound handlegraph::step_handle_t... Generating docs for compound handlegraph::net_handle_t... Generating docs for compound handlegraph::number_bool_packing... Generating docs for namespace handlegraph::algorithms Generating docs for compound handlegraph::algorithms::SubHandleGraph... Generating docs for namespace haplo Generating docs for compound haplo::int_itvl_t... Generating docs for compound haplo::gbwt_thread_t... Generating docs for compound haplo::hDP_gbwt_graph_accessor... Generating docs for compound haplo::haplo_DP_rectangle... Generating docs for compound haplo::haplo_DP_column... Generating docs for compound haplo::haplo_DP... Generating docs for compound haplo::linear_haplo_structure... Generating docs for nested compound haplo::linear_h/build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.hpp:53: warning: Found unknown command '@SQ' /build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.hpp:88: warning: Unsupported xml/html tag found aplo_structure::linearUnrepresentable... Generating docs for nested compound haplo::linear_haplo_structure::SNVvector... Generating docs for compound haplo::ScoreProvider... Generating docs for compound haplo::GBWTScoreProvider... Generating docs for compound haplo::LinearScoreProvider... Generating docs for namespace haplo::haploMath Generating docs for compound haplo::haploMath::RRMemo... Generating docs for namespace std Generating docs for compound std::hash< pair< A, B > >... Generating docs for compound std::hash< std::tuple< TT... > >... Generating docs for compound std::hash< vg::NodeSide >... Generating docs for compound std::hash< vg::NodeTraversal >... Generating docs for compound std::iterator_traits< vg::PhasedGenome::iterator >... Generating docs for compound std::hash< const vg::Snarl >... Generating docs for compound std::hash< handlegraph::handle_t >... Generating docs for compound std::hash< handlegraph::path_handle_t >... Generating docs for compound std::hash< handlegraph::step_handle_t >... Generating docs for compound std::hash< handlegraph::net_handle_t >... Generating docs for compound std::hash< handlegraph::edge_t >... Generating docs for namespace vg Generating docs for compound vg::BaseAligner... Generating docs for compound vg::GSSWAligner... Generating docs for compound vg::Aligner... Generating docs for compound vg::QualAdjAligner... Generating docs for compound vg::AlignerClient... Generating docs for compound vg::Annotation... Generating docs for compound vg::NoAlignmentInBandException... Generating docs for compound vg::BandedGlobalAligner... Generating docs for nested compound vg::BandedGlobalAligner::AltTracebackStack... Generating docs for nested compound vg::BandedGlobalAligner::AltTracebackStack::Deflection... Generating docs for nested compound vg::BandedGlobalAligner::BABuilder... Generating docs for nested compound vg::BandedGlobalAligner::BAMatrix... Generating docs for compound vg::BenchmarkResult... Generating docs for compound vg::CactusSide... Generating docs for compound vg::CactusSnarlFinder... Generating docs for compound vg::PathChunker... Generating docs for compound vg::ShuffledPairs... Generating docs for nested compound vg::ShuffledPairs::iterator... Generating docs for compound vg::MEMChainModelVertex... Generating docs for compound vg::MEMChainModel... Generating docs for compound vg::MEMClusterer... Generating docs for nested compound vg::MEMClusterer::DPScoreComparator... Generating docs for nested compound vg::MEMClusterer::HitEdge... Generating docs for nested compound vg::MEMClusterer::HitGraph... Generating docs for nested compound vg::MEMClusterer::HitNode... Generating docs for compound vg::NullClusterer... Generating docs for compound vg::OrientedDistanceMeasurer... Generating docs for compound vg::PathOrientedDistanceMeasurer... Generating docs for compound vg::SnarlOrientedDistanceMeasurer... Generating docs for compound vg::OrientedDistanceClusterer... Generating docs for compound vg::DistanceHeuristic... Generating docs for compound vg::SnarlMinDistance... Generating docs for compound vg::TipAnchoredMaxDistance... Generating docs for compound vg::TargetValueSearch... Generating docs for compound vg::TVSClusterer... Generating docs for compound vg::MinDistanceClusterer... Generating docs for compound vg::GreedyMinDistanceClusterer... Generating docs for compound vg::ComponentMinDistanceClusterer... Generating docs for compound vg::Colors... Generating docs for compound vg::ConstructedChunk... Generating docs for compound vg::Constructor... Generating docs for compound vg::DagifiedGraph... Generating docs for compound vg::Deconstructor... Generating docs for compound vg::DeletionAligner... Generating docs for compound vg::DinucleotideMachine... Generating docs for compound vg::DozeuInterface... Generating docs for nested compound vg::DozeuInterface::graph_pos_s... Generating docs for nested compound vg::DozeuInterface::OrderedGraph... Generating docs for compound vg::XdropAligner... Generating docs for compound vg::QualAdjXdropAligner... Generating docs /build/reproducible-path/vg-1.30.0+ds/src/filter.cpp:939: warning: Unsupported xml/html tag found for compound vg::DozeuPinningOverlay... Generating docs for compound vg::endianness... Generating docs for compound vg::ExtraNodeGraph... Generating docs for compound vg::FeatureSet... Generating docs for nested compound vg::FeatureSet::Feature... Generating docs for compound vg::Filter... Generating docs for compound vg::FlowSort... Generating docs for nested compound vg::FlowSort::Growth... Generating docs for nested compound vg::FlowSort::WeightedGraph... Generating docs for compound vg::Funnel... Generating docs for nested compound vg::Funnel::FilterPerformance... Generating docs for nested compound vg::Funnel::Item... Generating docs for nested compound vg::Funnel::Stage... Generating docs for compound vg::state_hash... Generating docs for compound vg::GaplessExtension... Generating docs for compound vg::GaplessExtender... Generating docs for compound vg::GBWTHandler... Generating docs for compound vg::SnarlState... Generating docs for compound vg::GenomeStateCommand... Generating docs for compound vg::InsertHaplotypeCommand... Generating docs for compound vg::DeleteHaplotypeCommand... Generating docs for compound vg::SwapHaplotypesCommand... Generating docs for compound vg::AppendHaplotypeCommand... Generating docs for compound vg::ReplaceSnarlHaplotypeCommand... Generating docs for compound vg::ReplaceLocalHaplotypeCommand... Generating docs for compound vg::GenomeState... Generating docs for compound vg::ConsistencyCalculator... Generating docs for compound vg::TraversalSupportCalculator... Generating docs for compound vg::GenotypeLikelihoodCalculator... Generating docs for compound vg::GenotypePriorCalculator... Generating docs for compound vg::VcfRecordConverter... Generating docs for compound vg::VcfRecordFilter... Generating docs for compound vg::AugmentedGraph... Generating docs for compound vg::SupportAugmentedGraph... Generating docs for compound vg::SimpleConsistencyCalculator... Generating docs for compound vg::FixedGenotypePriorCalculator... Generating docs for compound vg::SimpleTraversalSupportCalculator... Generating docs for compound vg::Genotyper... Generating docs for nested compound vg::Genotyper::Affinity... Generating docs for nested compound vg::Genotyper::hash_ambiguous_allele_set... Generating docs for nested compound vg::Genotyper::hash_node_traversal... Generating docs for nested compound vg::Genotyper::hash_oriented_edge... Generating docs for compound vg::GFFRecord... Generating docs for compound vg::GFFReader... Generating docs for compound vg::GraphCaller... Generating docs for compound vg::VCFOutputCaller... Generating docs for compound vg::GAFOutputCaller... Generating docs for compound vg::VCFGenotyper... Generating docs for compound vg::LegacyCaller... Generating docs for compound vg::FlowCaller... Generating docs for compound vg::GraphSynchronizer... Generating docs for nested compound vg::GraphSynchronizer::Lock... Generating docs for compound vg::wang_hash< handle_t >... Generating docs for compound vg::wang_hash< path_handle_t >... Generating docs for compound vg::HaplotypeIndexer... Generating docs for compound vg::wang_hash... Generating docs for compound vg::wang_hash< T * >... Generating docs for compound vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >... Generating docs for compound vg::wang_hash< std::pair< A, B > >... Generating docs for compound vg::hash_map... Generating docs for compound vg::string_hash_map... Generating docs for compound vg::pair_hash_map... Generating docs for compound vg::hash_map< K *, V >... Generating docs for compound vg::hash_set... Generating docs for compound vg::string_hash_set... Generating docs for compound vg::pair_hash_set... Generating docs for compound vg::hash_set< K * >... Generating docs for compound vg::Homogenizer... Generating docs for compound vg::HTSWriter... Generating docs for compound vg::HTSAlignmentEmitter... Generating docs for compound vg::SplicedHTSAlignmentEmitter... Generating docs for compound vg::IdentityOverlay... Generating docs for compound vg::IncrementalSubgraph... Generating docs for compound vg::IndexManager... Generating docs for compound vg::IndexingParameters... Generating docs for compound vg::VGIndexes... Generating docs for compound vg::IndexRegistry... Generating docs for compound vg::IndexFile... Generating docs for compound vg::IndexRecipe... Generating docs for compound vg::InsufficientInputException... Generating docs for compound vg::IndexedVG... Generating docs for nested compound vg::IndexedVG::CacheEntry... Generating docs for compound vg::IntegratedSnarlFinder... Generating docs for nested compound vg::IntegratedSnarlFinder::MergedAdjacencyGraph... Generating docs for compound vg::kmer_t... Generating docs for compound vg::AlignmentChainModelVertex... Generating docs for compound vg::AlignmentChainModel... Generating docs for compound vg::FragmentLengthDistribution... Generating docs for compound vg::PairedEndMapper... Generating docs for compound vg::BaseMapper... Generating docs for compound vg::FragmentLengthStatistics... Generating docs for compound vg::Mapper... Generating docs for compound vg::MCMCCaller... Generating docs for compound vg::MCMCGenotyper... Generating docs for compound vg::MaximalExactMatch... Generating docs for compound vg::MemoizingGraph... Generating docs for compound vg::MinimumDistanceIndex... Generating docs for nested compound vg::MinimumDistanceIndex::ChainIndex... Generating docs for nested compound vg::MinimumDistanceIndex::SnarlIndex... Generating docs for compound vg::MIPayload... Generating docs for compound vg::MinimizerMapper... Generating docs for nested compound vg::MinimizerMapper::Minimizer... Generating docs for compound vg::MSAConverter... Generating docs for compound vg::MultipathProblem... Generating docs for compound vg::connection_t... Generating docs for compound vg::subpath_t... Generating docs for compound vg::multipath_alignment_t... Generating docs for compound vg::MultipathAlignmentEmitter... Generating docs for compound vg::PathNode... Generating docs for compound vg::MultipathAlignmentGraph... Generating docs for compound vg::MultipathMapper... Generating docs for compound vg::NameMapper... Generating docs for compound vg::NestedTraversalFinder... Generating docs for compound vg::NodeSide... Generating docs for compound vg::wang_hash< NodeSide >... Generating docs for compound vg::NodeTraversal... Generating docs for compound vg::wang_hash< NodeTraversal >... Generating docs for compound vg::NullMaskingGraph... Generating docs for compound vg::OptionInterface... Generating docs for compound vg::Configurable... Generating docs for compound vg::ConfigurableParser... Generating docs for compound vg::OptionValueParser... Generating docs for compound vg::OptionValueParser< vector< Item > >... Generating docs for compound vg::BaseOption... Generating docs for compound vg::Option... Generating docs for compound vg::Option< vector< Item >, Parser >... Generating docs for compound vg::Packer... Generating docs for compound vg::Packers... Generating docs for compound vg::mapping_t... Generating docs for compound vg::Paths... Generating docs for compound vg::edit_t... Generating docs for compound vg::path_mapping_t... Generating docs for compound vg::path_t... Generating docs for compound vg::PathComponentIndex... Generating docs for compound vg::PathIndex... Generating docs for compound vg::PathSubgraph... Generating docs for compound vg::PathBranch... Generating docs for compound vg::PhaseUnfolder... Generating docs for compound vg::PhasedGenome... Generating docs for nested compound vg::PhasedGenome::Haplotype... Generating docs for nested compound vg::PhasedGenome::HaplotypeNode... Generating docs for nested compound vg::PhasedGenome::iterator... Generating docs for compound vg::Pictographs... Generating docs for compound vg::position_t... Generating docs for compound vg::Progressive... Generating docs for compound vg::RareVariantSimplifier... Generating docs for compound vg::ReadFilter... Generating docs for compound vg::Counts... Generating docs for compound vg::Region... Generating docs for compound vg::RegionExpander... Generating docs for compound vg::ReverseGraph... Generating docs for compound vg::Sampler... Generating docs for compound vg::NGSSimulator... Generating docs for nested compound vg::NGSSimulator::MarkovDistribution... Generating docs for compound vg::PositionIDScanner... Generating docs for compound vg::IDScanner... Generating docs for compound vg::WrappingPositionScanner... Generating docs for compound vg::SnarlSeedClusterer... Generating docs for nested compound vg::SnarlSeedClusterer::Cluster... Generating docs for nested compound vg::SnarlSeedClusterer::NetgraphNode... Generating docs for nested compound vg::SnarlSeedClusterer::NodeClusters... Generating docs for nested compound vg::SnarlSeedClusterer::Seed... Generating docs for nested compound vg::SnarlSeedClusterer::TreeState... Generating docs for compound vg::SeqComplexity... Generating docs for compound vg::SmallBitset... Generating docs for compound vg::SmallSnarlSimplifier... Generating docs for compound vg::SnarlCaller... Generating docs for nested compound vg::SnarlCaller::CallInfo... Generating docs for compound vg::SupportBasedSnarlCaller... Generating docs for compound vg::RatioSupportSnarlCaller... Generating docs for compound vg::PoissonSupportSnarlCaller... Generating docs for nested compound vg::PoissonSupportSnarlCaller::PoissonCallInfo... Generating docs for compound vg::SnarlFinder... Generating docs for compound vg::HandleGraphSnarlFinder... Generating docs for compound vg::ChainIterator... Generating docs for compound vg::NetGraph... Generating docs for compound vg::SnarlManager... Generating docs for nested compound vg::SnarlManager::SnarlRecord... Generating docs for compound vg::SourceSinkOverlay... Generating docs for compound vg::SpliceMotifs... Generating docs for compound vg::SpliceRegion... Generating docs for compound vg::JoinedSpliceGraph... Generating docs for compound vg::StrandSplitGraph... Generating docs for compound vg::BREAKPOINT... Generating docs for compound vg::DepthMap... Generating docs for compound vg::SRPE... Generating docs for compound vg::SSWAligner... Generating docs for compound vg::uniform_real_distribution... Generating docs for compound vg::normal_distribution... Generating docs for compound vg::WideningPRNG... Generating docs for compound vg::uniform_int_distribution... Generating docs for compound vg::discrete_distribution... Generating docs for compound vg::BitString... Generating docs for compound vg::BitStringTree... Generating docs for nested compound vg::BitStringTree::TreeNode... Generating docs for compound vg::StreamIndexBase... Generating docs for compound vg::StreamIndex... Generating docs for compound vg::StreamSorter... Generating docs for compound vg::SubHandleGraph... Generating docs for compound vg::SubgraphOverlay... Generating docs for compound vg::PathSubgraphOverlay... Generating docs for compound vg::SurjectingAlignmentEmitter... Generating docs for compound vg::Surjector... Generating docs for compound vg::Exon... Generating docs for compound vg::Transcript... Generating docs for compound vg::TranscriptPath... Generating docs for compound vg::EditedTranscriptPath... Generating docs for compound vg::CompletedTranscriptPath... Generating docs for compound vg::Transcriptome... Generating docs for compound vg::Translator... Generating docs for compound vg::TraversalFinder... Generating docs for compound vg::ExhaustiveTraversalFinder... Generating docs for compound vg::SupportRestrictedTraversalFinder... Generating docs for compound vg::ReadRestrictedTraversalFinder... Generating docs for compound vg::PathRestrictedTraversalFinder... Generating docs for compound vg::PathBasedTraversalFinder... Generating docs for compound vg::PathTraversalFinder... Generating docs for compound vg::TrivialTraversalFinder... Generating docs for compound vg::RepresentativeTraversalFinder... Generating docs for compound vg::VCFTraversalFinder... Generating docs for compound vg::FlowTraversalFinder... Generating docs for compound vg::GBWTTraversalFinder... Generating docs for compound vg::TraversalSupportFinder... Gene/build/reproducible-path/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'mismatches' could not be resolved /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag found rating docs for compound vg::PackedTraversalSupportFinder... Generating docs for compound vg::CachedPackedTraversalSupportFinder... Generating docs for compound vg::TreeSubgraph... Generating docs for compound vg::TreeNode... Generating docs for compound vg::Tree... Generating docs for compound vg::IncrementIter... Generating docs for compound vg::VariantAdder... Generating docs for compound vg::VcfBuffer... Generating docs for compound vg::WindowedVcfBuffer... Generating docs for compound vg::Version... Generating docs for compound vg::KmerPosition... Generating docs for compound vg::VG... Generating docs for nested compound vg::VG::Plan... Generating docs for compound vg::VGset... Generating docs for compound vg::Viz... Generating docs for compound vg::Watchdog... Generating docs for nested compound vg::Watchdog::thread_state_t... Generating docs for compound vg::Range... Generating docs for compound vg::is_instantiation_of... Generating docs for compound vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate >... Generating docs for compound vg::Graph... Generating docs for compound vg::Node... Generating docs for compound vg::Edge... Generating docs for compound vg::Edit... Generating docs for compound vg::Mapping... Generating docs for compound vg::Position... Generating docs for compound vg::Path... Generating docs for compound vg::Alignment... Generating docs for compound vg::MultipathAlignment... Generating docs for compound vg::Subpath... Generating docs for compound vg::Connection... Generating docs for compound vg::KmerMatch... Generating docs for compound vg::BasePileup... Generating docs for compound vg::NodePileup... Generating docs for compound vg::EdgePileup... Generating docs for compound vg::Pileup... Generating docs for compound vg::Snarl... Generating docs for compound vg::Visit... Generating docs for compound vg::SnarlTraversal... Generating docs for compound vg::Locus... Generating docs for compound vg::Genotype... Generating docs for compound vg::Support... Generating docs for compound vg::LocationSupport... Generating docs for compound vg::Translation... Generating docs for namespace vg::algorithms Generating docs for compound vg::algorithms::GFAFormatError... Generating docs for compound vg::algorithms::kmer_t... Generating docs for compound vg::algorithms::walk_t... Generating docs for namespace vg::io Generating docs for compound vg::io::ConvertedHashGraph... Generating docs for compound vg::io::JSONStreamHelper... Generating docs for compound vg::io::hFILE_cppstream... Generating docs for compound vg::io::AlignmentEmitter... Generating docs for compound vg::io::NullAlignmentEmitter... Generating docs for compound vg::io::TSVAlignmentEmitter... Generating docs for compound vg::io::VGAlignmentEmitter... Generating docs for compound vg::io::GafAlignmentEmitter... Generating docs for compound vg::io::BlockedGzipInputStream... Generating docs for compound vg::io::BlockedGzipOutputStream... Generating docs for compound vg::io::fdoutbuf... Generating docs for compound vg::io::fdostream... Generating docs for compound vg::io::fdinbuf... Generating docs for compound vg::io::fdistream... Generating docs for compound vg::io::streaminbuf... Generating docs for compound vg::io::streamistream... Generating docs for compound vg::io::MessageEmitter... Generating docs for compound vg::io::MessageIterator... Generating docs for compound vg::io::ProtobufEmitter... Generating docs for compound vg::io::ProtobufIterator... Generating docs for compound vg::io::Registry... Generating docs for nested compound vg::io::Registry::Tables... Generating docs for compound vg::io::StreamMultiplexer... Generating docs for compound vg::io::VPKG... Generating docs for namespace vg::subcommand Generating docs for compound vg::subcommand::Subcommand... Generating docs for namespace vg::temp_file Generating docs for compound vg::temp_file::Handler... Generating docs for namespace vg::unittest Generating docs for namespace xg Generating docs for compound xg::XGFormatError... Generating docs for compound xg::XG... Generati/build/reproducible-path/vg-1.30.0+ds/src/banded_global_aligner.hpp:88: warning: Unsupported xml/html tag found ng docs for compound xg::XGPath... Generating docs for namespace xg::temp_file Generating docs for compound xg::temp_file::Handler... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class vg::Genotyper::Affinity Generating XML output for class vg::Aligner Generating XML output for class vg::AlignerClient Generating XML output for class vg::Alignment Generating XML output for class vg::AlignmentChainModel Generating XML output for class vg::AlignmentChainModelVertex Generating XML output for class vg::io::AlignmentEmitter Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack Generating XML output for class vg::Annotation Generating XML output for class vg::AppendHaplotypeCommand Generating XML output for class vg::AugmentedGraph Generating XML output for class vg::BandedGlobalAligner::BABuilder Generating XML output for class vg::BandedGlobalAligner::BAMatrix Generating XML output for class vg::BandedGlobalAligner Generating XML output for class vg::BaseAligner Generating XML output for class vg::BaseMapper Generating XML output for class vg::BaseOption Generating XML output for class vg::BasePileup Generating XML output for class vg::BenchmarkResult Generating XML output for class vg::BitString Generating XML output for class vg::BitStringTree Generating XML output for class vg::io::BlockedGzipInputStream Generating XML output for class vg::io::BlockedGzipOutputStream Generating XML output for class handlegraph::BoolReturningWrapper Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, Iterated, bool > Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, Iterated, void > Generating XML output for class vg::BREAKPOINT Generating XML output for class handlegraph::BuildableSnarlDecomposition Generating XML output for class vg::CachedPackedTraversalSupportFinder Generating XML output for class vg::IndexedVG::CacheEntry Generating XML output for class vg::CactusSide Generating XML output for class vg::CactusSnarlFinder Generating XML output for class vg::SnarlCaller::CallInfo Generating XML output for class vg::MinimumDistanceIndex::ChainIndex Generating XML output for class vg::ChainIterator Generating XML output for class vg::SnarlSeedClusterer::Cluster Generating XML output for class vg::Colors Generating XML output for class vg::CompletedTranscriptPath Generating XML output for class vg::ComponentMinDistanceClusterer Generating XML output for class vg::Configurable Generating XML output for class vg::ConfigurableParser Generating XML output for class vg::Connection Generating XML output for class vg::connection_t Generating XML output for class vg::ConsistencyCalculator Generating XML output for class vg::ConstructedChunk Generating XML output for class vg::Constructor Generating XML output for class vg::io::ConvertedHashGraph Generating XML output for class vg::Counts Generating XML output for class vg::DagifiedGraph Generating XML output for class vg::Deconstructor Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack::Deflection Generating XML output for class handlegraph::DeletableHandleGraph Generating XML output for class vg::DeleteHaplotypeCommand Generating XML output for class vg::DeletionAligner Generating XML output for class vg::DepthMap Generating XML output for class vg::DinucleotideMachine Generating XML output for class vg::discrete_distribution Generating XML output for class vg::DistanceHeuristic Generating XML output for class vg::DozeuInterface Generating XML output for class vg::DozeuPinningOverlay Generating XML output for class /build/reproducible-path/vg-1.30.0+ds/src/filter.cpp:939: warning: Unsupported xml/html tag found vg::MEMClusterer::DPScoreComparator Generating XML output for class vg::Edge Generating XML output for class vg::EdgePileup Generating XML output for class vg::Edit Generating XML output for class vg::edit_t Generating XML output for class vg::EditedTranscriptPath Generating XML output for class vg::endianness Generating XML output for class vg::ExhaustiveTraversalFinder Generating XML output for class vg::Exon Generating XML output for class handlegraph::ExpandingOverlayGraph Generating XML output for class vg::ExtraNodeGraph Generating XML output for class vg::io::fdinbuf Generating XML output for class vg::io::fdistream Generating XML output for class vg::io::fdostream Generating XML output for class vg::io::fdoutbuf Generating XML output for class vg::FeatureSet::Feature Generating XML output for class vg::FeatureSet Generating XML output for class vg::Filter Generating XML output for class vg::Funnel::FilterPerformance Generating XML output for class vg::FixedGenotypePriorCalculator Generating XML output for class vg::FlowCaller Generating XML output for class vg::FlowSort Generating XML output for class vg::FlowTraversalFinder Generating XML output for class vg::FragmentLengthDistribution Generating XML output for class vg::FragmentLengthStatistics Generating XML output for class vg::Funnel Generating XML output for class vg::io::GafAlignmentEmitter Generating XML output for class vg::GAFOutputCaller Generating XML output for class gafkluge::GafRecord Generating XML output for class gafkluge::GafStep Generating XML output for class vg::GaplessExtender Generating XML output for class vg::GaplessExtension Generating XML output for class haplo::gbwt_thread_t Generating XML output for class vg::GBWTHandler Generating XML output for class haplo::GBWTScoreProvider Generating XML output for class vg::GBWTTraversalFinder Generating XML output for class vg::GenomeState Generating XML output for class vg::GenomeStateCommand Generating XML output for class vg::Genotype Generating XML output for class vg::GenotypeLikelihoodCalculator Generating XML output for class vg::GenotypePriorCalculator Generating XML output for class vg::Genotyper Generating XML output for class vg::algorithms::GFAFormatError Generating XML output for class vg::GFFReader Generating XML output for class vg::GFFRecord Generating XML output for class vg::Graph Generating XML output for class vg::DozeuInterface::graph_pos_s Generating XML output for class vg::GraphCaller Generating XML output for class vg::GraphSynchronizer Generating XML output for class vg::GreedyMinDistanceClusterer Generating XML output for class vg::FlowSort::Growth Generating XML output for class vg::GSSWAligner Generating XML output for class handlegraph::handle_t Generating XML output for class handlegraph::HandleGraph Generating XML output for class vg::HandleGraphSnarlFinder Generating XML output for class vg::temp_file::Handler Generating XML output for class xg::temp_file::Handler Generating XML output for class haplo::haplo_DP Generating XML output for class haplo::haplo_DP_column Generating XML output for class haplo::haplo_DP_rectangle Generating XML output for class vg::PhasedGenome::Haplotype Generating XML output for class vg::HaplotypeIndexer Generating XML output for class vg::PhasedGenome::HaplotypeNode Generating XML output for class std::hash< const vg::Snarl > Generating XML output for class std::hash< handlegraph::edge_t > Generating XML output for class std::hash< handlegraph::handle_t > Generating XML output for class std::hash< handlegraph::net_handle_t > Generating XML output for class std::hash< handlegraph::path_handle_t > Generating XML output for class std::hash< handlegraph::step_handle_t > Generating XML output for class std::hash< pair< A, B > > Generating XML output for class std::hash< std::tuple< TT... > > Generating XML output for class std::hash< vg::NodeSide > Generating XML output for class std::hash< vg::NodeTraversal > Generating XML output for class vg::Genotyper::hash_ambiguous_allele_set Generating XML output for class vg::hash_map Generating XML output for class vg::hash_map< K *, V > Generating XML output for class vg::Genotyper::hash_node_traversal Generating XML output for class vg::Genotyper::hash_oriented_edge Generating XML output for class vg::hash_set Generating XML output for class vg::hash_set< K * > Generating XML output for class haplo::hDP_gbwt_graph_accessor Generating XML output for class hFILE_backend Generating XML output for class vg::io::hFILE_cppstream Generating XML output for class vg::MEMClusterer::HitEdge Generating XML output for class vg::MEMClusterer::HitGraph Generating XML output for class vg::MEMClusterer::HitNode Generating XML output for class vg::Homogenizer Generating XML output for class vg::HTSAlignmentEmitter Generating XML output for class vg::HTSWriter Generating XML output for class vg::IdentityOverlay Generating XML output for class vg::IDScanner Generating XML output for class vg::IncrementalSubgraph Generating XML output for class vg::IncrementIter Generating XML output for class vg::IndexedVG Generating XML output for class vg::IndexFile Generating XML output for class vg::IndexingParameters Generating XML output for class vg::IndexManager Generating XML output for class vg::IndexRecipe Generating XML output for class vg::IndexRegistry Generating XML output for class vg::InsertHaplotypeCommand Generating XML output for class vg::InsufficientInputException Generating XML output for class haplo::int_itvl_t Generating XML output for class vg::IntegratedSnarlFinder Generating XML output for class vg::is_instantiation_of Generating XML output for class vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate > Generating XML output for class vg::Funnel::Item Generating XML output for class handlegraph::PathForEachSocket::iterator Generating XML output for class vg::PhasedGenome::iterator Generating XML output for class vg::ShuffledPairs::iterator Generating XML output for class std::iterator_traits< vg::PhasedGenome::iterator > Generating XML output for class j2pb_error Generating XML output for class job_type Generating XML output for class vg::JoinedSpliceGraph Generating XML output for class json_autoptr Generating XML output for class vg::io::JSONStreamHelper Generating XML output for class vg::algorithms::kmer_t Generating XML output for class vg::kmer_t Generating XML output for class vg::KmerMatch Generating XML output for class vg::KmerPosition Generating XML output for class vg::LegacyCaller Generating XML output for class haplo::linear_haplo_structure Generating XML output for class haplo::LinearScoreProvider Generating XML output for class haplo::linear_haplo_structure::linearUnrepresentable Generating XML output for class vg::LocationSupport Generating XML output for class vg::GraphSynchronizer::Lock Generating XML output for class vg::Locus Generating XML output for class vg::Mapper Generating XML output for class vg::Mapping Generating XML output for class vg::mapping_t Generating XML output for class vg::NGSSimulator::MarkovDistribution Generating XML output for class vg::MaximalExactMatch Generating XML output for class vg::MCMCCaller Generating XML output for class vg::MCMCGenotyper Generating XML output for class vg::MEMChainModel Generating XML output for class vg::MEMChainModelVertex Generating XML output for class vg::MEMClusterer Generating XML output for class vg::MemoizingGraph Generating XML output for class vg::IntegratedSnarlFinder::MergedAdjacencyGraph Generating XML output for class vg::io::MessageEmitter Generating XML output for class vg::io::MessageIterator Generating XML output for class vg::MinDistanceClusterer Generating XML output for class vg::MinimizerMapper::Minimizer Generating XML output for class vg::MinimizerMapper Generating XML output for class vg::MinimumDistanceIndex Generating XML output for class vg::MIPayload Generating XML output for class vg::MSAConverter Generating XML output for class vg::multipath_alignment_t Generating XML output for class vg::MultipathAlignment Generating XML output for class vg::MultipathAlignmentEmitter Generating XML output for class vg::MultipathAlignmentGraph Generating XML output for class vg::MultipathMapper Generating XML output for class vg::MultipathProblem Generating XML output for class handlegraph::MutableHandleGraph Generating XML output for class handlegraph::MutablePathDeletableHandleGraph Generating XML output for class handlegraph::MutablePathHandleGraph Generating XML output for class handlegraph::MutablePathMutableHandleGraph Generating XML output for class vg::NameMapper Generating XML output for class vg::NestedTraversalFinder Generating XML output for class handlegraph::net_handle_t Generating XML output for class vg::NetGraph Generating XML output for class vg::SnarlSeedClusterer::NetgraphNode Generating XML output for class vg::NGSSimulator Generating XML output for class vg::NoAlignmentInBandException Generating XML output for class vg::Node Generating XML output for class vg::SnarlSeedClusterer::NodeClusters Generating XML output for class vg::NodePileup Generating XML output for class vg::NodeSide Generating XML output for class vg::NodeTraversal Generating XML output for class vg::normal_distribution Generating XML output for class vg::io::NullAlignmentEmitter Generating XML output for class vg::NullClusterer Generating XML output for class vg::NullMaskingGraph Generating XML output for class handlegraph::number_bool_packing Generating XML output for class vg::Option Generating XML output for class vg::Option< vector< Item >, Parser > Generating XML output for class vg::OptionInterface Generating XML output for class vg::OptionValueParser Generating XML output for class vg::OptionValueParser< vector< Item > > Generating XML output for class vg::DozeuInterface::OrderedGraph Generating XML output for class vg::OrientedDistanceClusterer Generating XML output for class vg::OrientedDistanceMeasurer Generating XML output for class vg::PackedTraversalSupportFinder Generating XML output for class vg::Packer Generating XML output for class vg::Packers Generating XML output for class vg::pair_hash_map Generating XML output for class vg::pair_hash_set Generating XML output for class vg::PairedEndMapper Generating XML output for class vg::Path Generating XML output for class handlegraph::path_handle_t Generating XML output for class vg::path_mapping_t Generating XML output for class vg::path_t Generating XML output for class vg::PathBasedTraversalFinder Generating XML output for class vg::PathBranch Generating XML output for class vg::PathChunker Generating XML output for class vg::PathComponentIndex Generating XML output for class handlegraph::PathForEachSocket Generating XML output for class handlegraph::PathHandleGraph Generating XML output for class vg::PathIndex Generating XML output for class vg::PathNode Generating XML output for class vg::PathOrientedDistanceMeasurer Generating XML output for class handlegraph::PathPositionHandleGraph Generating XML output for class vg::PathRestrictedTraversalFinder Generating XML output for class vg::Paths Generating XML output for class vg::PathSubgraph Generating XML output for class vg::PathSubgraphOverlay Generating XML output for class vg::PathTraversalFinder Generating XML output for class vg::PhasedGenome Generating XML output for class vg::PhaseUnfolder Generating XML output for class vg::Pictographs Generating XML output for class vg::Pileup Generating XML output for class vg::VG::Plan Generating XML output for class vg::PoissonSupportSnarlCaller::PoissonCallInfo Generating XML output for class vg::PoissonSupportSnarlCaller Generating XML output for class vg::Position Generating XML output for class vg::position_t Generating XML output for class vg::PositionIDScanner Generating XML output for class vg::Progressive Generating XML output for class vg::io::ProtobufEmitter Generating XML output for class vg::io::ProtobufIterator Generating XML output for class PruningParameters Generating XML output for class vg::QualAdjAligner Generating XML output for class vg::QualAdjXdropAligner Generating XML output for class vg::Range Generating XML output for class handlegraph::RankedHandleGraph Gene/build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/vg.proto:267: warning: Unsupported xml/html tag found rating XML output for class vg::RareVariantSimplifier Generating XML output for class vg::RatioSupportSnarlCaller Generating XML output for class vg::ReadFilter Generating XML output for class vg::ReadRestrictedTraversalFinder Generating XML output for class vg::Region Generating XML output for class vg::RegionExpander Generating XML output for class vg::io::Registry Generating XML output for class vg::ReplaceLocalHaplotypeCommand Generating XML output for class vg::ReplaceSnarlHaplotypeCommand Generating XML output for class vg::RepresentativeTraversalFinder Generating XML output for class vg::ReverseGraph Generating XML output for class haplo::haploMath::RRMemo Generating XML output for class vg::Sampler Generating XML output for class haplo::ScoreProvider Generating XML output for class vg::SnarlSeedClusterer::Seed Generating XML output for class vg::SeqComplexity Generating XML output for class handlegraph::Serializable Generating XML output for class handlegraph::SerializableHandleGraph Generating XML output for class vg::ShuffledPairs Generating XML output for class vg::SimpleConsistencyCalculator Generating XML output for class vg::SimpleTraversalSupportCalculator Generating XML output for class vg::SmallBitset Generating XML output for class vg::SmallSnarlSimplifier Generating XML output for class vg::Snarl Generating XML output for class vg::SnarlCaller Generating XML output for class handlegraph::SnarlDecomposition Generating XML output for class vg::SnarlFinder Generating XML output for class vg::MinimumDistanceIndex::SnarlIndex Generating XML output for class vg::SnarlManager Generating XML output for class vg::SnarlMinDistance Generating XML output for class vg::SnarlOrientedDistanceMeasurer Generating XML output for class vg::SnarlManager::SnarlRecord Generating XML output for class vg::SnarlSeedClusterer Generating XML output for class vg::SnarlState Generating XML output for class vg::SnarlTraversal Generating XML output for class haplo::linear_haplo_structure::SNVvector Generating XML output for class vg::SourceSinkOverlay Generating XML output for class vg::SplicedHTSAlignmentEmitter Generating XML output for class vg::SpliceMotifs Generating XML output for class vg::SpliceRegion Generating XML output for class vg::SRPE Generating XML output for class vg::SSWAligner Generating XML output for class vg::Funnel::Stage Generating XML output for class vg::state_hash Generating XML output for class handlegraph::step_handle_t Generating XML output for class vg::StrandSplitGraph Generating XML output for class vg::io::streaminbuf Generating XML output for class vg::StreamIndex Generating XML output for class vg::StreamIndexBase Generating XML output for class vg::io::streamistream Generating XML output for class vg::io::StreamMultiplexer Generating XML output for class vg::StreamSorter Generating XML output for class vg::string_hash_map Generating XML output for class vg::string_hash_set Generating XML output for class vg::subcommand::Subcommand Generating XML output for class vg::SubgraphOverlay Generating XML output for class handlegraph::algorithms::SubHandleGraph Generating XML output for class vg::SubHandleGraph Generating XML output for class vg::Subpath Generating XML output for class vg::subpath_t Generating XML output for class vg::Support Generating XML output for class vg::SupportAugmentedGraph Generating XML output for class vg::SupportBasedSnarlCaller Generating XML output for class vg::SupportRestrictedTraversalFinder Generating XML output for class vg::SurjectingAlignmentEmitter Generating XML output for class vg::Surjector Generating XML output for class vg::SwapHaplotypesCommand Generating XML output for class vg::io::Registry::Tables Generating XML output for class vg::TargetValueSearch Generating XML output for class vg::Watchdog::thread_state_t Generating XML output for class vg::TipAnchoredMaxDistance Generating XML output for class vg::Transcript Generating XML output for class vg::Transcriptome Generating XML output for class vg::TranscriptPath Generating XML output for class vg::Translat/build/reproducible-path/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.30.0+ds/src/vg.hpp:894: warning: explicit link request to 'mismatches' could not be resolved /build/reproducible-path/vg-1.30.0+ds/src/hts_alignment_emitter.hpp:53: warning: Found unknown command '@SQ' ion Generating XML output for class vg::Translator Generating XML output for class vg::TraversalFinder Generating XML output for class vg::TraversalSupportCalculator Generating XML output for class vg::TraversalSupportFinder Generating XML output for class vg::Tree Generating XML output for class vg::BitStringTree::TreeNode Generating XML output for class vg::TreeNode Generating XML output for class vg::SnarlSeedClusterer::TreeState Generating XML output for class vg::TreeSubgraph Generating XML output for class handlegraph::TriviallySerializable Generating XML output for class vg::TrivialTraversalFinder Generating XML output for class vg::io::TSVAlignmentEmitter Generating XML output for class vg::TVSClusterer Generating XML output for class vg::uniform_int_distribution Generating XML output for class vg::uniform_real_distribution Generating XML output for class vg::VariantAdder Generating XML output for class vg::VcfBuffer Generating XML output for class vg::VCFGenotyper Generating XML output for class vg::VCFOutputCaller Generating XML output for class vg::VcfRecordConverter Generating XML output for class vg::VcfRecordFilter Generating XML output for class vg::VCFTraversalFinder Generating XML output for class handlegraph::VectorizableHandleGraph Generating XML output for class Vectorizer Generating XML output for class vg::Version Generating XML output for class vg::VG Generating XML output for class vg::io::VGAlignmentEmitter Generating XML output for class vg::VGIndexes Generating XML output for class vg::VGset Generating XML output for class vg::Visit Generating XML output for class vg::Viz Generating XML output for class vg::io::VPKG Generating XML output for class vg::algorithms::walk_t Generating XML output for class vg::wang_hash Generating XML output for class vg::wang_hash< handle_t > Generating XML output for class vg::wang_hash< NodeSide > Generating XML output for class vg::wang_hash< NodeTraversal > Generating XML output for class vg::wang_hash< path_handle_t > Generating XML output for class vg::wang_hash< std::pair< A, B > > Generating XML output for class vg::wang_hash< T * > Generating XML output for class vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > Generating XML output for class vg::Watchdog Generating XML output for class vg::FlowSort::WeightedGraph Generating XML output for class vg::WideningPRNG Generating XML output for class vg::WindowedVcfBuffer Generating XML output for class vg::WrappingPositionScanner Generating XML output for class vg::XdropAligner Generating XML output for class xg::XG Generating XML output for class xg::XGFormatError Generating XML output for class xg::XGPath Generating XML output for namespace @452 Generating XML output for namespace bdsg Generating XML output for namespace gafkluge Generating XML output for namespace gfak Generating XML output for namespace google Generating XML output for namespace google::protobuf Generating XML output for namespace google::protobuf::io Generating XML output for namespace handlegraph Generating XML output for namespace handlegraph::algorithms Generating XML output for namespace haplo Generating XML output for namespace haplo::haploMath Generating XML output for namespace sdsl Generating XML output for namespace spp Generating XML output for namespace std Generating XML output for namespace std::@79 Generating XML output for namespace structures Generating XML output for namespace vg Generating XML output for namespace vg::algorithms Generating XML output for namespace vg::io Generating XML output for namespace vg::subcommand Generating XML output for namespace vg::temp_file Generating XML output for namespace vg::unittest Generating XML output for namespace xg Generating XML output for namespace xg::temp_file Generating XML output for file append_graph.cpp Generating XML output for file apply_orientations.cpp Generating XML output for file are_equivalent.cpp Generating XML output for file copy_graph.cpp Generating XML output for file count_walks.cpp Generating XML output for file dagify.cpp Generating XML output for file deletable_handle_graph.cpp Generating XML output for file dijkstra.cpp Generating XML output for file eades_algorithm.cpp Generating XML output for file extend.cpp Generating XML output for file find_shortest_paths.cpp Generating XML output for file find_tips.cpp Generating XML output for file handle_graph.cpp Generating XML output for file buildable_snarl_decomposition.hpp Generating XML output for file deletable_handle_graph.hpp Generating XML output for file expanding_overlay_graph.hpp Generating XML output for file handle_graph.hpp Generating XML output for file iteratee.hpp Generating XML output for file mutable_handle_graph.hpp Generating XML output for file mutable_path_deletable_handle_graph.hpp Generating XML output for file mutable_path_handle_graph.hpp Generating XML output for file mutable_path_mutable_handle_graph.hpp Generating XML output for file path_handle_graph.hpp Generating XML output for file path_position_handle_graph.hpp Generating XML output for file serializable.hpp Generating XML output for file serializable_handle_graph.hpp Generating XML output for file snarl_decomposition.hpp Generating XML output for file trivially_serializable.hpp Generating XML output for file util.hpp Generating XML output for file is_acyclic.cpp Generating XML output for file is_single_stranded.cpp Generating XML output for file mutable_handle_graph.cpp Generating XML output for file path_handle_graph.cpp Generating XML output for file path_position_handle_graph.cpp Generating XML output for file ranked_handle_graph.cpp Generating XML output for file reverse_complement.cpp Generating XML output for file serializable.cpp Generating XML output for file snarl_decomposition.cpp Generating XML output for file split_strands.cpp Generating XML output for file strongly_connected_components.cpp Generating XML output for file topological_sort.cpp Generating XML output for file trivially_serializable.cpp Generating XML output for file types.cpp Generating XML output for file unchop.cpp Generating XML output for file weakly_connected_components.cpp Generating XML output for file vg.proto Generating XML output for file alignment_emitter.hpp Generating XML output for file alignment_io.hpp Generating XML output for file basic_stream.hpp Generating XML output for file blocked_gzip_input_stream.hpp Generating XML output for file blocked_gzip_output_stream.hpp Generating XML output for file edit.hpp Generating XML output for file fdstream.hpp Generating XML output for file gafkluge.hpp Generating XML output for file hfile_cppstream.hpp Generating XML output for file hfile_internal.hpp Generating XML output for file json2pb.h Generating XML output for file loader.hpp Generating XML output for file message_emitter.hpp Generating XML output for file message_iterator.hpp Generating XML output for file protobuf_emitter.hpp Generating XML output for file protobuf_iterator.hpp Generating XML output for file registry.hpp Generating XML output for file stream.hpp Generating XML output for file stream_multiplexer.hpp Generating XML output for file vpkg.hpp Generating XML output for file alignment_emitter.cpp Generating XML output for file alignment_io.cpp Generating XML output for file basic_stream.cpp Generating XML output for file bin2ascii.h Generating XML output for file blocked_gzip_input_stream.cpp Generating XML output for file blocked_gzip_output_stream.cpp Generating XML output for file edit.cpp Generating XML output for file hfile_cppstream.cpp Generating XML output for file json2pb.cpp Generating XML output for file message_emitter.cpp Generating XML output for file message_iterator.cpp Generating XML output for file registry.cpp Generating XML output for file stream.cpp Generating XML output for file stream_multiplexer.cpp Generating XML output for file vpkg.cpp Generating XML output for file xg.cpp Generating XML output for file xg.hpp Generating XML output for file a_star.hpp Generating XML output for file alignment_path_offsets.cpp Generating XML output for file alignment_path_offsets.hpp Generating XML output for file approx_path_distance.cpp Generating XML output for file approx_path_distance.hpp Generating XML output for file coverage_depth.cpp Generating XML output for file coverage_depth.hpp Generating XML output for file dfs.cpp Generating XML output for file dfs.hpp Generating XML output for file disjoint_components.cpp Generating XML output for file disjoint_components.hpp Generating XML output for file distance_to_head.cpp Generating XML output for file distance_to_head.hpp Generating XML output for file distance_to_tail.cpp Generating XML output for file distance_to_tail.hpp Generating XML output for file expand_context.cpp Generating XML output for file expand_context.hpp Generating XML output for file extract_connecting_graph.cpp Generating XML output for file extract_connecting_graph.hpp Generating XML output for file extract_containing_graph.cpp Generating XML output for file extract_containing_graph.hpp Generating XML output for file extract_extending_graph.cpp Generating XML output for file extract_extending_graph.hpp Generating XML output for file gfa_to_handle.cpp Generating XML output for file gfa_to_handle.hpp Generating XML output for file id_sort.cpp Generating XML output for file id_sort.hpp Generating XML output for file jump_along_path.cpp Generating XML output for file jump_along_path.hpp Generating XML output for file k_widest_paths.cpp Generating XML output for file k_widest_paths.hpp Generating XML output for file merge.cpp Generating XML output for file merge.hpp Generating XML output for file nearest_offsets_in_paths.cpp Generating XML output for file nearest_offsets_in_paths.hpp Generating XML output for file next_pos_chars.cpp Generating XML output for file next_pos_chars.hpp Generating XML output for file normalize.cpp Generating XML output for file normalize.hpp Generating XML output for file path_string.cpp Generating XML output for file path_string.hpp Generating XML output for file prune.cpp Generating XML output for file prune.hpp Generating XML output for file ref_path_distance.cpp Generating XML output for file ref_path_distance.hpp Generating XML output for file shortest_cycle.cpp Generating XML output for file shortest_cycle.hpp Generating XML output for file simplify_siblings.cpp Generating XML output for file simplify_siblings.hpp Generating XML output for file sorted_id_ranges.cpp Generating XML output for file sorted_id_ranges.hpp Generating XML output for file three_edge_connected_components.cpp Generating XML output for file three_edge_connected_components.hpp Generating XML output for file to_gfa.cpp Generating XML output for file to_gfa.hpp Generating XML output for file walk.cpp Generating XML output for file walk.hpp Generating XML output for file aligner.cpp Generating XML output for file aligner.hpp Generating XML output for file alignment.cpp Generating XML output for file alignment.hpp Generating XML output for file annotation.hpp Generating XML output for file augment.cpp Generating XML output for file augment.hpp Generating XML output for file banded_global_aligner.cpp Generating XML output for file banded_global_aligner.hpp Generating XML output for file benchmark.cpp Generating XML output for file benchmark.hpp Generating XML output for file build_index.cpp Generating XML output for file build_index.hpp Generating XML output for file cactus.cpp Generating XML output for file cactus.hpp Generating XML output for file cactus_snarl_finder.cpp Generating XML output for file cactus_snarl_finder.hpp Generating XML output for file chunker.cpp Generating XML output for file chunker.hpp Generating XML output for file cluster.cpp Generating XML output for file cluster.hpp Generating XML output for file colors.hpp Generating XML output for file constructor.cpp Generating XML output for file constructor.hpp Generating XML output for file convert.hpp Generating XML output for file crash.cpp Generating XML output for file crash.hpp Generating XML output for file dagified_graph.cpp Generating XML output for file dagified_graph.hpp Generating XML output for file deconstructor.cpp Generating XML output for file deconstructor.hpp Generating XML output for file deletion_aligner.cpp Generating XML output for file deletion_aligner.hpp Generating XML output for file dinucleotide_machine.cpp Generating XML output for file dinucleotide_machine.hpp Generating XML output for file dozeu_interface.cpp Generating XML output for file dozeu_interface.hpp Generating XML output for file dozeu_pinning_overlay.cpp Generating XML output for file dozeu_pinning_overlay.hpp Generating XML output for file endianness.hpp Generating XML output for file entropy.cpp Generating XML output for file entropy.hpp Generating XML output for file extra_node_graph.cpp Generating XML output for file extra_node_graph.hpp Generating XML output for file feature_set.cpp Generating XML output for file feature_set.hpp Generating XML output for file filter.cpp Generating XML output for file filter.hpp Generating XML output for file flow_sort.cpp Generating XML output for file flow_sort.hpp Generating XML output for file funnel.cpp Generating XML output for file funnel.hpp Generating XML output for file gapless_extender.cpp Generating XML output for file gapless_extender.hpp Generating XML output for file gbwt_helper.cpp Generating XML output for file gbwt_helper.hpp Generating XML output for file genome_state.cpp Generating XML output for file genome_state.hpp Generating XML output for file genotypekit.cpp Generating XML output for file genotypekit.hpp Generating XML output for file genotyper.cpp Generating XML output for file genotyper.hpp Generating XML output for file gfa.cpp Generating XML output for file gfa.hpp Generating XML output for file gff_reader.cpp Generating XML output for file gff_reader.hpp Generating XML output for file graph.cpp Generating XML output for file graph.hpp Generating XML output for file graph_caller.cpp Generating XML output for file graph_caller.hpp Generating XML output for file graph_synchronizer.cpp Generating XML output for file graph_synchronizer.hpp Generating XML output for file handle.hpp Generating XML output for file haplotype_extracter.cpp Generating XML output for file haplotype_extracter.hpp Generating XML output for file haplotype_indexer.cpp Generating XML output for file haplotype_indexer.hpp Generating XML output for file haplotypes.cpp Generating XML output for file haplotypes.hpp Generating XML output for file hash_map.hpp Generating XML output for file homogenizer.cpp Generating XML output for file homogenizer.hpp Generating XML output for file hts_alignment_emitter.cpp Generating XML output for file hts_alignment_emitter.hpp Generating XML output for file identity_overlay.cpp Generating XML output for file identity_overlay.hpp Generating XML output for file incremental_subgraph.cpp Generating XML output for file incremental_subgraph.hpp Generating XML output for file index_manager.cpp Generating XML output for file index_manager.hpp Generating XML output for file index_registry.cpp Generating XML output for file index_registry.hpp Generating XML output for file indexed_vg.cpp Generating XML output for file indexed_vg.hpp Generating XML output for file integrated_snarl_finder.cpp Generating XML output for file integrated_snarl_finder.hpp Generating XML output for file converted_hash_graph.hpp Generating XML output for file json_stream_helper.hpp Generating XML output for file load_proto_to_graph.cpp Generating XML output for file load_proto_to_graph.hpp Generating XML output for file register_libvg_io.cpp Generating XML output for file register_libvg_io.hpp Generating XML output for file register_loader_saver_distance_index.cpp Generating XML output for file register_loader_saver_distance_index.hpp Generating XML output for file register_loader_saver_gbwt.cpp Generating XML output for file register_loader_saver_gbwt.hpp Generating XML output for file register_loader_saver_gbwtgraph.cpp Generating XML output for file register_loader_saver_gbwtgraph.hpp Generating XML output for file register_loader_saver_gcsa.cpp Generating XML output for file register_loader_saver_gcsa.hpp Generating XML output for file register_loader_saver_hash_graph.cpp Generating XML output for file register_loader_saver_hash_graph.hpp Generating XML output for file register_loader_saver_lcp.cpp Generating XML output for file register_loader_saver_lcp.hpp Generating XML output for file register_loader_saver_minimizer.cpp Generating XML output for file register_loader_saver_minimizer.hpp Generating XML output for file register_loader_saver_odgi.cpp Generating XML output for file register_loader_saver_odgi.hpp Generating XML output for file register_loader_saver_packed_graph.cpp Generating XML output for file register_loader_saver_packed_graph.hpp Generating XML output for file register_loader_saver_r_index.cpp Generating XML output for file register_loader_saver_r_index.hpp Generating XML output for file register_loader_saver_snarl_manager.cpp Generating XML output for file register_loader_saver_snarl_manager.hpp Generating XML output for file register_loader_saver_vg.cpp Generating XML output for file register_loader_saver_vg.hpp Generating XML output for file register_loader_saver_xg.cpp Generating XML output for file register_loader_saver_xg.hpp Generating XML output for file save_handle_graph.hpp Generating XML output for file kmer.cpp Generating XML output for file kmer.cpp Generating XML output for file kmer.hpp Generating XML output for file kmer.hpp Generating XML output for file main.cpp Generating XML output for file mapper.cpp Generating XML output for file mapper.hpp Generating XML output for file mcmc_caller.cpp Generating XML output for file mcmc_caller.hpp Generating XML output for file mcmc_genotyper.cpp Generating XML output for file mcmc_genotyper.hpp Generating XML output for file mem.cpp Generating XML output for file mem.hpp Generating XML output for file memoizing_graph.cpp Generating XML output for file memoizing_graph.hpp Generating XML output for file memusage.cpp Generating XML output for file memusage.hpp Generating XML output for file min_distance.cpp Generating XML output for file min_distance.hpp Generating XML output for file minimizer_mapper.cpp Generating XML output for file minimizer_mapper.hpp Generating XML output for file msa_converter.cpp Generating XML output for file msa_converter.hpp Generating XML output for file multipath_alignment.cpp Generating XML output for file multipath_alignment.hpp Generating XML output for file multipath_alignment_emitter.cpp Generating XML output for file multipath_alignment_emitter.hpp Generating XML output for file multipath_alignment_graph.cpp Generating XML output for file multipath_alignment_graph.hpp Generating XML output for file multipath_mapper.cpp Generating XML output for file multipath_mapper.hpp Generating XML output for file name_mapper.cpp Generating XML output for file name_mapper.hpp Generating XML output for file nested_traversal_finder.cpp Generating XML output for file nested_traversal_finder.hpp Generating XML output for file nodeside.hpp Generating XML output for file nodetraversal.hpp Generating XML output for file null_masking_graph.cpp Generating XML output for file null_masking_graph.hpp Generating XML output for file option.cpp Generating XML output for file option.hpp Generating XML output for file packer.cpp Generating XML output for file packer.hpp Generating XML output for file path.cpp Generating XML output for file path.hpp Generating XML output for file path_component_index.cpp Generating XML output for file path_component_index.hpp Generating XML output for file path_index.cpp Generating XML output for file path_index.hpp Generating XML output for file path_subgraph.cpp Generating XML output for file path_subgraph.hpp Generating XML output for file phase_unfolder.cpp Generating XML output for file phase_unfolder.hpp Generating XML output for file phased_genome.cpp Generating XML output for file phased_genome.hpp Generating XML output for file pictographs.hpp Generating XML output for file position.cpp Generating XML output for file position.hpp Generating XML output for file preflight.cpp Generating XML output for file preflight.hpp Generating XML output for file progressive.cpp Generating XML output for file progressive.hpp Generating XML output for file qual_adj_xdrop_aligner.cpp Generating XML output for file rare_variant_simplifier.cpp Generating XML output for file rare_variant_simplifier.hpp Generating XML output for file readfilter.cpp Generating XML output for file readfilter.hpp Generating XML output for file region.cpp Generating XML output for file region.hpp Generating XML output for file region_expander.cpp Generating XML output for file region_expander.hpp Generating XML output for file reverse_graph.cpp Generating XML output for file reverse_graph.hpp Generating XML output for file sampler.cpp Generating XML output for file sampler.hpp Generating XML output for file scanner.cpp Generating XML output for file scanner.hpp Generating XML output for file seed_clusterer.cpp Generating XML output for file seed_clusterer.hpp Generating XML output for file sequence_complexity.hpp Generating XML output for file small_bitset.hpp Generating XML output for file small_snarl_simplifier.cpp Generating XML output for file small_snarl_simplifier.hpp Generating XML output for file snarl_caller.cpp Generating XML output for file snarl_caller.hpp Generating XML output for file snarls.cpp Generating XML output for file snarls.hpp Generating XML output for file source_sink_overlay.cpp Generating XML output for file source_sink_overlay.hpp Generating XML output for file splicing.cpp Generating XML output for file splicing.hpp Generating XML output for file split_strand_graph.cpp Generating XML output for file split_strand_graph.hpp Generating XML output for file srpe.cpp Generating XML output for file srpe.hpp Generating XML output for file ssw_aligner.cpp Generating XML output for file ssw_aligner.hpp Generating XML output for file statistics.cpp Generating XML output for file statistics.hpp Generating XML output for file stream_index.cpp Generating XML output for file stream_index.hpp Generating XML output for file stream_sorter.cpp Generating XML output for file stream_sorter.hpp Generating XML output for file add_main.cpp Generating XML output for file align_main.cpp Generating XML output for file annotate_main.cpp Generating XML output for file augment_main.cpp Generating XML output for file autoindex_main.cpp Generating XML output for file benchmark_main.cpp Generating XML output for file call_main.cpp Generating XML output for file chunk_main.cpp Generating XML output for file circularize_main.cpp Generating XML output for file cluster_main.cpp Generating XML output for file combine_main.cpp Generating XML output for file concat_main.cpp Generating XML output for file construct_main.cpp Generating XML output for file convert_main.cpp Generating XML output for file deconstruct_main.cpp Generating XML output for file depth_main.cpp Generating XML output for file dotplot_main.cpp Generating XML output for file explode_main.cpp Generating XML output for file filter_main.cpp Generating XML output for file find_main.cpp Generating XML output for file gamcompare_main.cpp Generating XML output for file gampcompare_main.cpp Generating XML output for file gamsort_main.cpp Generating XML output for file gbwt_main.cpp Generating XML output for file genotype_main.cpp Generating XML output for file giraffe_main.cpp Generating XML output for file help_main.cpp Generating XML output for file ids_main.cpp Generating XML output for file index_main.cpp Generating XML output for file inject_main.cpp Generating XML output for file join_main.cpp Generating XML output for file kmers_main.cpp Generating XML output for file map_main.cpp Generating XML output for file mcmc_main.cpp Generating XML output for file minimizer_main.cpp Generating XML output for file mod_main.cpp Generating XML output for file mpmap_main.cpp Generating XML output for file msga_main.cpp Generating XML output for file pack_main.cpp Generating XML output for file paths_main.cpp Generating XML output for file prune_main.cpp Generating XML output for file recalibrate_main.cpp Generating XML output for file rna_main.cpp Generating XML output for file sift_main.cpp Generating XML output for file sim_main.cpp Generating XML output for file simplify_main.cpp Generating XML output for file snarls_main.cpp Generating XML output for file sort_main.cpp Generating XML output for file srpe_main.cpp Generating XML output for file stats_main.cpp Generating XML output for file subcommand.cpp Generating XML output for file subcommand.hpp Generating XML output for file surject_main.cpp Generating XML output for file test_main.cpp Generating XML output for file trace_main.cpp Generating XML output for file translate_main.cpp Generating XML output for file validate_main.cpp Generating XML output for file vectorize_main.cpp Generating XML output for file version_main.cpp Generating XML output for file view_main.cpp Generating XML output for file viz_main.cpp Generating XML output for file subgraph.cpp Generating XML output for file subgraph.cpp Generating XML output for file subgraph.hpp Generating XML output for file subgraph.hpp Generating XML output for file subgraph_overlay.cpp Generating XML output for file subgraph_overlay.hpp Generating XML output for file surjecting_alignment_emitter.cpp Generating XML output for file surjecting_alignment_emitter.hpp Generating XML output for file surjector.cpp Generating XML output for file surjector.hpp Generating XML output for file swap_remove.hpp Generating XML output for file transcriptome.cpp Generating XML output for file transcriptome.hpp Generating XML output for file translator.cpp Generating XML output for file translator.hpp Generating XML output for file traversal_finder.cpp Generating XML output for file traversal_finder.hpp Generating XML output for file traversal_support.cpp Generating XML output for file traversal_support.hpp Generating XML output for file tree_subgraph.cpp Generating XML output for file tree_subgraph.hpp Generating XML output for file types.hpp Generating XML output for file types.hpp Generating XML output for file driver.cpp Generating XML output for file driver.hpp Generating XML output for file utility.cpp Generating XML output for file utility.hpp Generating XML output for file variant_adder.cpp Generating XML output for file variant_adder.hpp Generating XML output for file variant_recall.cpp Generating XML output for file variant_recall.hpp Generating XML output for file vcf_buffer.cpp Generating XML output for file vcf_buffer.hpp Generating XML output for file vectorizer.cpp Generating XML output for file vectorizer.hpp Generating XML output for file version.cpp Generating XML output for file version.hpp Generating XML output for file vg.cpp Generating XML output for file vg.hpp Generating XML output for file vg_set.cpp Generating XML output for file vg_set.hpp Generating XML output for file viz.cpp Generating XML output for file viz.hpp Generating XML output for file wang_hash.hpp Generating XML output for file watchdog.cpp Generating XML output for file watchdog.hpp Generating XML output for file xdrop_aligner.cpp Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/src/algorithms/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/deps/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/handlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/include/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/src/io/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/io/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/src/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/xg/src/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/src/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libhandlegraph/src/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/src/subcommand/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/src/unittest/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/libvgio/include/vg/ Generate XML output for dir /build/reproducible-path/vg-1.30.0+ds/deps/xg/ Running plantuml with JAVA... lookup cache used 12549/65536 hits=86853 misses=14307 finished... echo "View documentation at: file:///build/reproducible-path/vg-1.30.0+ds/doc/doxygen/index.html" View documentation at: file:///build/reproducible-path/vg-1.30.0+ds/doc/doxygen/index.html make[2]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' make[1]: Leaving directory '/build/reproducible-path/vg-1.30.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/vg-1.30.0+ds' export PATH=$PATH:/build/reproducible-path/vg-1.30.0+ds/debian/help \ && . /build/reproducible-path/vg-1.30.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.30.0+ds/test && prove -v t/ ) index file /tmp/vg-0P0i8u/vg-mcNdet.fai not found, generating... index file /tmp/vg-0P0i8u/vg-R0Cqjs.fai not found, generating... index file /tmp/vg-0P0i8u/vg-JNsmcu.fai not found, generating... index file /tmp/vg-0P0i8u/vg-snVXYr.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SVTYPE=DEL GT ! index file /tmp/vg-0P0i8u/vg-TX5q4v.fai not found, generating... index file /tmp/vg-0P0i8u/vg-rCancw.fai not found, generating... index file /tmp/vg-0P0i8u/vg-m57Iiv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-FW64Ds.fai not found, generating... index file /tmp/vg-0P0i8u/vg-3O5vpv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-TUPM7v.fai not found, generating... index file /tmp/vg-0P0i8u/vg-tzTIuu.fai not found, generating... index file /tmp/vg-0P0i8u/vg-UyXEnw.fai not found, generating... index file /tmp/vg-0P0i8u/vg-TOAL2u.fai not found, generating... index file /tmp/vg-0P0i8u/vg-dJn2Kv.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SPAN=19;SVLEN=-19;SVTYPE=DEL GT END: 29 SVLEN: -19 index file /tmp/vg-0P0i8u/vg-tZst0u.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SPAN=19;SVLEN=-19;SVTYPE=DEL GT END: 29 SVLEN: -19 index file /tmp/vg-0P0i8u/vg-gv8JIv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-7hE53s.fai not found, generating... index file /tmp/vg-0P0i8u/vg-LUbeOu.fai not found, generating... index file /tmp/vg-0P0i8u/vg-eCHPlu.fai not found, generating... index file /tmp/vg-0P0i8u/vg-IH4gQr.fai not found, generating... index file /tmp/vg-0P0i8u/vg-4AlNZs.fai not found, generating... index file /tmp/vg-0P0i8u/vg-dTi2bv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-M27I7s.fai not found, generating... index file /tmp/vg-0P0i8u/vg-0TX4ds.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=18;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 18 POS: 9 index file /tmp/vg-0P0i8u/vg-p790ls.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=18;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 18 POS: 9 index file /tmp/vg-0P0i8u/vg-A06Rks.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=13;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-0P0i8u/vg-wMVDas.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=13;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-0P0i8u/vg-wbyuFv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-T2rQ0s.fai not found, generating... index file /tmp/vg-0P0i8u/vg-SOrTjv.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-0P0i8u/vg-Jaja0v.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-0P0i8u/vg-8zWCwv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-rQzvlt.fai not found, generating... index file /tmp/vg-0P0i8u/vg-Aeikuv.fai not found, generating... index file /tmp/vg-0P0i8u/vg-hIsnBt.fai not found, generating... Warning: Cactus does not currently support finding snarls in a single-node connected component Warning: Cactus does not currently support finding snarls in a single-node connected component Warning: Cactus does not currently support finding snarls in a single-node connected component Warning: Cactus does not currently support finding snarls in a single-node connected component Warning: Cactus does not currently support finding snarls in a single-node connected component Warning: Cactus does not currently support finding snarls in a single-node connected component t/00_unittest.t ....... 1..1 =============================================================================== All tests passed (8246463 assertions in 497 test cases) ok 1 - vg unit tests complete successfully ok t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... error:[vg::Constructor] non-ATGCN characters found in variant: x 973 . G A,* 99 . AC=2;LEN=1;NA=2;NS=1;TYPE=snp index file tiny/ambiguous.fa.fai not found, generating... warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. t/02_vg_construct.t ... 1..28 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges ok 7 - node size is manageable by default ok 8 - construction of a very complex region succeeds ok 9 - the complex graph has the expected number of nodes ok 10 - the complex graph has the expected number of edges ok 11 - the ordering of variants at the same position has no effect on the resulting graph ok 12 - construction does not fail when the first position in the VCF is repeated and has an indel ok 13 - the size of the regions used in construction has no effect on the graph ok 14 - the number of threads used in construction has no effect on the graph ok 15 - the number of threads and regions used in construction has no effect on the graph ok 16 - construction of a graph with two head nodes succeeds ok 17 - the graph contains all the sequence in the reference and VCF ok 18 - varying the max node size does not affect graph length ok 19 - nodes are correctly capped in size ok 20 - -R --region flag is respected ok 21 - vg construct does not require a vcf ok 22 - vg construct respects node size limit ok 23 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 24 - vg constructs the correct graph for inversions ok 25 - vg construct skips variants with . ALTs ok 26 - VCF with * alleles is rejected ok 27 - Reference with ambiguity codes has them coerced to Ns ok 28 - Expected number of Ns are created ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Ml7nBv/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_iU3O9B/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_55JMar/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/03_vg_view.t ........ 1..19 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM not ok 5 - view can round-trip JSON and GAM # got: '5b9458e2d6d1f262977b932998bb8d3a -' # expected: '7d450e53c0870ff504f33af188613e5d -' Binary files x.vg and - differ not ok 6 - view can reconstruct a VG graph from JSON # got: '1' # expected: '0' ok 7 - view can pass through VG when loading as vg::VG ok 8 - view can pass through semantically identical VG normally ok 9 - view parses sample names ok 10 - view can handle fastq input not ok 11 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' ok 12 - view outputs properly oriented GFA ok 13 - view produces the expected number of lines of dot output from a cyclic graph ok 14 - streaming JSON output produces the expected number of chunks ok 15 - duplicate warnings can be suppressed when loading as vg::VG ok 16 - gfa graphs with overlaps are rejected ok 17 - GFA import produces a concise error message when overlaps are present ok 18 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 19 - GFA import produces a concise error message in that case Failed 3/19 subtests [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/04_vg_align.t ....... 1..20 ok 1 - alignment traverses the correct path ok 2 - alignment score is as expected ok 3 - full length bonus works and is included by default ok 4 - bonuses are included on only one end for pinned alignments ok 5 - scoring parameters are respected ok 6 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 7 - alignment does not contain excessive soft clips under lenient scoring ok 8 - score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring ok 9 - alignment score does not overflow at 255 when using 8x16bit vectors ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors ok 11 - Ns do not cause excessive soft clipping ok 12 - nodes are only referenced if they have mappings ok 13 - align can use query names and outputs GAM ok 14 - alignment to cyclic graphs works ok 15 - graphs where duplicated nodes need flipping can be used for alignment ok 16 - node flipping doesn't destroy the alignment ok 17 - alignment correctly handles an inversion ok 18 - the exploding graph doesn't blow up ok 19 - pinning doesn't cause problems for gssw ok 20 - left pinning is correctly handled ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZrlxKl/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open test.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nGijhv/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open w.xg while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'combine' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Unreadable stream while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/05_vg_find.t ........ 1..27 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns ok 16 - the GAM index can return the set of alignments mapping to a node ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM ok 18 - the index can be queried using GAM alignments ok 19 - find gets connected edges between queried nodes by default ok 20 - find gets nodes provided in a node file list not ok 21 - extracting by path adds no extra edges # got: '' # expected: '1' not ok 22 - pattern based path extraction works # got: '0' # expected: '38' ok 23 - path DAG range query works ok 24 - we can extract a set of targets to separate files ok 25 - the same extraction can be made using BED input ok 26 - we see the expected number of kmers in the given targets ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 Failed 2/27 subtests WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated t/06_vg_index.t ....... 1..51 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - samples can be excluded from haplotype indexing ok 19 - excluded samples were not included in the GBWT index ok 20 - GBWT from GAF same as from GAM ok 21 - building GBWT index for a regional graph ok 22 - no warnings about missing variants produced ok 23 - building an XG index of multiple graphs ok 24 - building a GCSA index of multiple graphs ok 25 - building both indexes at once ok 26 - the indexes are identical ok 27 - building a GBWT index of multiple graphs with haplotypes ok 28 - building an XG index of multiple graphs with haplotypes ok 29 - building a GCSA index of multiple graphs with haplotypes ok 30 - building XG and GCSA indexes at once ok 31 - building an XG index with alt paths ok 32 - building a GBWT index from an XG index ok 33 - the indexes are identical ok 34 - GBWT can be built for paths ok 35 - fail with nonexistent file ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used ok 37 - vg index and vg gamsort produce identical sorted GAM indexes ok 38 - storage of multiple graphs in an index succeeds ok 39 - can index backward nodes ok 40 - can index kmers for backward nodes ok 41 - GCSA2 index works on cyclic graphs with heads and tails ok 42 - GCSA2 index works on cyclic graphs with no heads or tails ok 43 - GCSA2 index works on cyclic graphs with self loops ok 44 - GCSA2 index works on general cyclic graphs ok 45 - GCSA2 indexing of a tiny graph works ok 46 - GCSA2 indexing succeeds on a single-node graph ok 47 - GCSA2 indexing succeeds on graph with heads but no tails ok 48 - a useful error message is produced when nodes are too large ok 49 - snarl finding with trivial snarls ok 50 - building a distance index of a graph ok 51 - building a distance index of a graph without maximum index ok [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kicHX8/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XajPrm/stacktrace.txt Please include the stack trace file in your bug report! index file t.fa.fai not found, generating... t/07_vg_map.t ......... 1..54 ok 1 - offset counts unused bases from the start of the node on the forward strand ok 2 - xdrop alignment obtains the expected result ok 3 - xdrop alignment obtains the expected result for the reverse complement ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand ok 5 - offset counts unused bases from the start of the node on the reverse strand ok 6 - global alignment traverses the correct path ok 7 - alignment score is as expected ok 8 - scoring parameters are respected ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 10 - full length bonus always be included ok 11 - full length bonus can be set to 0 ok 12 - vg map takes -d as input without a variant graph ok 13 - vg map can align across a SNP ok 14 - alignment works on a small graph ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities ok 17 - chunky-banded alignment works ok 18 - multiple alignments are returned in descending score order ok 19 - only a single primary alignment is returned ok 20 - mapping of BAM file produces expected number of alignments ok 21 - mapping from a fastq produces the expected number of alignments ok 22 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 23 - vg connects paired-end reads in gam output ok 24 - mapping to graphs that can't be oriented without swapping edges works correctly ok 25 - reads multi-map to multiple possible locations ok 26 - vg map works based on gcsa and xg indexes ok 27 - the mapping quality may be capped ok 28 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 29 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 30 - only primary alignments have mapping quality scores ok 31 - unpaired reads produce mapping quality scores ok 32 - map returns same output on xg and vg (single threaded) ok 33 - base quality adjusted alignment produces higher scores if mismatches have low quality ok 34 - error on vg map -f (unpaired) ok 35 - error on vg map -f (interleaved) ok 36 - error on vg map -f (paired, LHS) ok 37 - error on vg map -f (paired, RHS) ok 38 - mapping a read that touches unused nodes gets the base score ok 39 - mapping a read that matches a haplotype gets a small penalty ok 40 - mapping a read that matches a haplotype with exponent 0 gets the base score ok 41 - mapping a read that matches no haplotypes gets a larger penalty not ok 42 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 43 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 44 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 45 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 46 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 47 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 48 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 49 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 50 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 51 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 52 - mapper can read FASTA input ok 53 - mapper can read multiline FASTA input ok 54 - xdrop works on a reversed read Failed 10/54 subtests t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs ok 4 - can sort and re-number a graph with self loops ok 5 - can sort and renumber a complex cyclic graph ok 6 - sorting removes back-edges in a DAG ok 7 - sorting assigns node IDs in topological order ok 8 - sorting does not affect id range ok 9 - sorting does not affect id range of vg ok 10 - sorting does not affect id range of hg ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8GO4rl/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes ok 2 - concat doubles the number of edges + 1 ok 3 - concat -p doubles the number of nodes on reversing graph not ok 4 - concat -p doubles the number of edges + 1 on reversing graph # got: '0' # expected: '1' Failed 1/4 subtests t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! t/10_vg_stats.t ....... 1..18 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct ok 8 - aligned read stats are computed correctly ok 9 - basic stats agree between graph formats ok 10 - stats can be computed for GAM files without graphs ok 11 - a path overlap description of a test graph has the expected length ok 12 - vg stats -F detects format of old protobuf graph ok 13 - vg stats -F detects format of newer protobuf graph ok 14 - vg stats -F detects format of hash graph ok 15 - vg stats -F detects format of packed graph ok 16 - vg stats -F detects format of odgi graph ok 17 - vg stats -F detects format of xg graph ok 18 - vg stats -D found correct degree distribution of tiny graph ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. t/11_vg_paths.t ....... 1..14 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - thread listing works from GBWT ok 4 - thread selection by name prefix works correctly ok 5 - thread selection by sample name works correctly ok 6 - no threads are reported for invalid samples ok 7 - vg paths may be used to extract threads ok 8 - vg paths may be used to extract threads as GAF ok 9 - Fasta extracted from xg is the same as the input fasta ok 10 - Fasta extracted from vg is the same as the input fasta ok 11 - Fasta extracted from threads has correct number of lines ok 12 - a single path may be retained ok 13 - path filtering does not modify the graph ok 14 - alt allele paths can be dropped ok WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok index file n.fa.fai not found, generating... warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz t/13_vg_sim.t ......... 1..34 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - reads can be simulated from all paths ok 10 - simulation was successful ok 11 - reads can be simulated from GBWT samples ok 12 - simulation was successful ok 13 - pairs simulated even when fragments overlap ok 14 - sim does not emit reads with Ns ok 15 - sim can emit reads with Ns when asked to ok 16 - sim doesn't emit Ns even with pair and errors ok 17 - Sample simulation works along with --any-path ok 18 - not having any regexes skips all unvisited contigs ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig ok 22 - multiple regexes are interpreted ok 23 - regexes are interpreted as regexes ok 24 - assigning a very high ploidy by regex starves out the other paths ok 25 - Sample simulation works along with --any-path with training FASTQ ok 26 - not having any regexes skips all unvisited contigs with training FASTQ ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ ok 30 - multiple regexes are interpreted with training FASTQ ok 31 - regexes are interpreted as regexes with training FASTQ ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ ok 33 - ngs trained simulator works ok 34 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 95 [algorithms::normalize] iteration 2 current length 95 [algorithms::normalize] normalized in 1 steps terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WWEfzS/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_z1rDu7/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JrjjaU/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_IWKgAN/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 106 [algorithms::normalize] iteration 2 current length 105 [algorithms::normalize] iteration 3 current length 105 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 103 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] iteration 3 current length 100 [algorithms::normalize] normalized in 2 steps t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works ok 5 - normalization produces the correct number of nodes ok 6 - normalization removes redundant SNP alleles ok 7 - normalization produces a valid graph ok 8 - looped normalization produces a valid graph ok 9 - unchop produces a valid graph ok 10 - normalization removes redundant sequence in the graph ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '1' # expected: '0' ok 14 - unchop correctly handles paths ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion ok 18 - mod successfully unchops a difficult graph ok 19 - chopping self-cycling nodes retains the cycle ok 20 - unrolling works and produces a valid graph ok 21 - unfolding works and produces a valid graph ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components ok 25 - unfold followed by dagify produces a graph with no cycles ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths ok 29 - dagify correctly calculates the minimum distance through the unrolled component ok 30 - dagify produces a graph of the correct size ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 2/32 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hYht6j/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3DJqs1/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XQZVtQ/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6Guaj0/stacktrace.txt Please include the stack trace file in your bug report! t/15_vg_surject.t ..... 1..33 ok 1 - reads are generated ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 4 - vg surject actually places reads on the correct path ok 5 - vg surject doesn't need to be told which path to use ok 6 - vg surject works for every read simulated from a dense graph ok 7 - vg surject spliced algorithm works for every read simulated from a dense graph ok 8 - vg surject produces valid SAM output ok 9 - vg map may surject reads to produce valid SAM output ok 10 - vg map may surject reads to produce valid BAM output not ok 11 - vg surject retains read names # got: '0' # expected: '100' ok 12 - vg surject can set sample and read group ok 13 - we respect the original mapping's softclips ok 14 - quality strings we will use for testing are oriented correctly ok 15 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags ok 16 - vg surject produces valid BAM output not ok 17 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 18 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' ok 19 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 25 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 26 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' ok 27 - surjection works for a longer (151bp) read ok 28 - surjection works for another difficult read ok 29 - mapping reproduces qualities from BAM input ok 30 - mapping reproduces qualities from fastq input ok 31 - mapping reproduces qualities from GAF input ok 32 - surject works on GAMP input ok 33 - surject works on paired GAMP input Failed 10/33 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/s-rev.fa.fai not found, generating... [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/inv.fa.fai not found, generating... [algorithms::normalize] iteration 1 current length 210 [algorithms::normalize] iteration 2 current length 210 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. t/16_vg_msga.t ........ 1..14 ok 1 - MSGA produces the expected graph for GRCh38 HLA-V ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V {"edge": [{"from": "5", "from_start": true, "to": "6", "to_end": true}, {"from": "5", "from_start": true, "to": "7", "to_end": true}, {"from": "6", "to": "7"}], "node": [{"id": "5", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "7", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "6", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "6"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "7"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "5"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "6"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "5"}, "rank": "2"}], "name": "s2"}]} ok 3 - soft clips at node boundaries (start) are included correctly ok 4 - soft clips at node boundaries (end) are included correctly ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph ok 7 - the paths of the graph encode the original sequences used to build it ok 8 - even when banding the paths of the graph encode the original sequences used to build it ok 9 - HLA K-3138 correctly includes all input paths ok 10 - a difficult cyclic path can be included to produce a valid graph ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected ok 12 - edges in cycles with two nodes are correctly included ok 13 - HLA B-3106 is assembled into a valid graph ok 14 - odd-sized overlaps may be used for chunked alignment ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vtf6OK/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1JLXY4/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file] could not open file "edits-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.m1.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found in augmented.gaf.vg while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Og7l30/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file] could not open file "edit-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/17_vg_augment.t ..... 1..39 not ok 1 - direct augmentation embeds reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 # got: '' # expected: '18' not ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes # got: '' # expected: '18' not ok 6 - direct augmentation embeds reads fully for probable errors # got: '0' # expected: '3' not ok 7 - adding a probable error by direct augmentation adds 3 more nodes # got: '' # expected: '18' ok 8 - path inclusion does not modify the graph when alignment is a perfect match ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold ok 11 - output GAM has single edit when SNP was filtered out due to coverage ok 12 - path inclusion with a complex variant introduces the right number of nodes ok 13 - path inclusion works for deletions ok 14 - SNPs can be included in the graph ok 15 - a soft clip at read start becomes a new head of the graph ok 16 - a soft clip at read end becomes a new tail of the graph ok 17 - augment -s works as desired ok 18 - the expected graph translation is exported when the graph is edited ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps ok 22 - augmenting with 2snps makes correct number of nodes ok 23 - low-quality snp is filtered ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph ok 26 - augmenting between nodes without filters works as expected ok 27 - augmenting between nodes with inactive filters works as expected ok 28 - augmenting between nodes N filter works as expected ok 29 - augmenting between nodes without filters works as expected on reverse strand ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand ok 31 - augmenting between nodes N filter works as expected on reverse strand ok 32 - augmenting within node without filters works as expected ok 33 - augmenting within node with inactive filters works as expected ok 34 - augmenting within node with N filter works as expected ok 35 - augmenting within node without filters works as expected on reverse strand ok 36 - augmenting within node with inactive filters works as expected on reverse strand ok 37 - augmenting within node with N filter works as expected on reverse strand ok 38 - sequence in filtered alignment has removed insertion ok 39 - sequence in filtered alignment has removed insertion on reverse strand Failed 7/39 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LXJJoo/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open tiny_aug.xg while loading handlegraph::HandleGraph error:[get_input_file] could not open file "tiny_aug.xg" index file inverting/miniFasta.fa.fai not found, generating... WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file m.fa.fai not found, generating... t/18_vg_call.t ........ 1..12 ok 1 - calling empty gam gives empty VCF ok 2 - Called microinversion ok 3 - Called no microinversion with haploid setting ok 4 - Fewer than 8 differences between called and true SV genotypes ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg ok 11 - vg call finds true homozygous variants in a cyclic graph ok 12 - vg call finds same variants when using gbwt to enumerate traversals ok t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BPCmpO/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tekCST/stacktrace.txt Please include the stack trace file in your bug report! t/21_vg_filter.t ...... 1..10 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - read pairs can be tropped by feature not ok 10 - read pairs can be kept if only one read fails # got: '0' # expected: '2' Failed 1/10 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps graph path 'alt2.3' invalid: edge from 15 end to 1 start does not exist [vg view] warning: graph is invalid! t/26_deconstruct.t .... 1..19 ok 1 - deconstruct retrieved original VCF (modulo adjacent snp allele) ok 2 - deconstructed hla vcf has correct number of sites ok 3 - deconstructed hla vcf has correct insertion ok 4 - deconstructed hla vcf with other path has correct number of sites ok 5 - deconstructed hla vcf has correct deletion ok 6 - path-based and exhaustive decontruction give equivalent sites when expected ok 7 - path that differs from reference in every alt has correct genotype ok 8 - path that is same as reference in every alt has correct genotype ok 9 - reference contig correctly written ok 10 - deconstruct correctly handles a simple inversion ok 11 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl ok 13 - deconstruct correctly handles a cycle in the alt path ok 14 - cyclic reference deconstruction has correct number of variants ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl ok 16 - -P -A options return correct number of variants ok 17 - -P -A options use correct reference name ok 18 - -P -A identifies conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 4 Snarl length distribution: 1 3 2 1 index file flat1.fa.fai not found, generating... index file flat2.fa.fai not found, generating... Statistics: Number of Non-Degenerate Snarls: 8 Snarls traversed by reads: 8 Snarls on reference: 0 Snarl length distribution: WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file flats.fa.fai not found, generating... terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Gccd84/stacktrace.txt Please include the stack trace file in your bug report! Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Statistics: Number of Non-Degenerate Snarls: 1 Snarls traversed by reads: 1 Snarls on reference: 1 Snarl length distribution: 0 1 t/27_vg_genotype.t .... 1..5 ok 1 - vg genotype runs successfully ok 2 - vg genotype runs successfully when emitting vcf ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON ok 5 - genotype finds big insert ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3HAF5i/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_72xUrP/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NgIp4q/stacktrace.txt Please include the stack trace file in your bug report! [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fWP7qD/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end t/30_vg_chunk.t ....... 1..24 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk has path going through node 9 ok 5 - -s produces correct number of chunks ok 6 - gam chunker produces correct number of graphs ok 7 - gam chunker produces correct number of gams ok 8 - gam chunker produces bed with correct number of chunks ok 9 - gam chunker emits each matching read at most once ok 10 - chunk contains the expected number of alignments ok 11 - id chunker produces correct chunk size ok 12 - id chunker produces correct single chunk ok 13 - id chunker traces correct chunk size ok 14 - chunker extracts no threads from an empty gPBWT ok 15 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 16 - chunker can extract a partial haplotype from a GBWT ok 17 - n-chunking works and chunks over the full graph ok 18 - path-based components finds subgraphs ok 19 - x gam chunk has correct number of reads ok 20 - y gam chunk has correct number of reads ok 21 - x gam chunk has correct number of reads with -p path ok 22 - y gam chunk has correct number of reads with -p path ok 23 - path-based component contains correct path length ok 24 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 1: 3 haplotypes at chrR:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at chrR:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at chrR:23: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/refN.fa.fai not found, generating... Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/ngap.fa.fai not found, generating... Variant 1: 2 haplotypes at ngap:10923: 224 bp vs. 224 bp haplotypes vs. graphs average Variant 2: 5 haplotypes at ngap:11014: 256 bp vs. 258 bp haplotypes vs. graphs average Variant 3: 5 haplotypes at ngap:11030: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 4: 5 haplotypes at ngap:11035: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 5: 5 haplotypes at ngap:11043: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 1: 2 haplotypes at x:9: 160 bp vs. 161 bp haplotypes vs. graphs average Variant 2: 2 haplotypes at x:10: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 3: 2 haplotypes at x:14: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 4: 2 haplotypes at x:34: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 5: 2 haplotypes at x:39: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 6: 2 haplotypes at x:52: 224 bp vs. 231 bp haplotypes vs. graphs average Variant 7: 2 haplotypes at x:58: 224 bp vs. 232 bp haplotypes vs. graphs average Variant 8: 2 haplotypes at x:100: 256 bp vs. 265 bp haplotypes vs. graphs average Variant 9: 2 haplotypes at x:103: 256 bp vs. 267 bp haplotypes vs. graphs average Variant 10: 2 haplotypes at x:122: 288 bp vs. 299 bp haplotypes vs. graphs average Variant 11: 2 haplotypes at x:142: 288 bp vs. 301 bp haplotypes vs. graphs average Variant 12: 2 haplotypes at x:160: 306 bp vs. 319 bp haplotypes vs. graphs average Variant 13: 2 haplotypes at x:172: 338 bp vs. 353 bp haplotypes vs. graphs average Variant 14: 2 haplotypes at x:178: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 15: 2 haplotypes at x:187: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 16: 2 haplotypes at x:200: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 17: 2 haplotypes at x:204: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 18: 2 haplotypes at x:218: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 19: 2 haplotypes at x:221: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 20: 2 haplotypes at x:272: 256 bp vs. 266 bp haplotypes vs. graphs average Variant 21: 2 haplotypes at x:277: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 22: 2 haplotypes at x:287: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 23: 2 haplotypes at x:294: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 24: 2 haplotypes at x:297: 291 bp vs. 305 bp haplotypes vs. graphs average Variant 25: 2 haplotypes at x:312: 323 bp vs. 340 bp haplotypes vs. graphs average Variant 26: 2 haplotypes at x:313: 323 bp vs. 341 bp haplotypes vs. graphs average Variant 27: 2 haplotypes at x:345: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 28: 2 haplotypes at x:347: 323 bp vs. 339 bp haplotypes vs. graphs average Variant 29: 2 haplotypes at x:353: 311 bp vs. 326 bp haplotypes vs. graphs average Variant 30: 2 haplotypes at x:373: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 31: 2 haplotypes at x:397: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 32: 2 haplotypes at x:398: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 33: 2 haplotypes at x:405: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 34: 2 haplotypes at x:408: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 35: 2 haplotypes at x:466: 254 bp vs. 260 bp haplotypes vs. graphs average Variant 36: 2 haplotypes at x:474: 286 bp vs. 295 bp haplotypes vs. graphs average Variant 37: 2 haplotypes at x:489: 286 bp vs. 296 bp haplotypes vs. graphs average Variant 38: 2 haplotypes at x:500: 286 bp vs. 297 bp haplotypes vs. graphs average Variant 39: 2 haplotypes at x:523: 300 bp vs. 309 bp haplotypes vs. graphs average Variant 40: 2 haplotypes at x:533: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 41: 1 haplotypes at x:553: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 42: 1 haplotypes at x:566: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 43: 2 haplotypes at x:629: 277 bp vs. 281 bp haplotypes vs. graphs average Variant 44: 2 haplotypes at x:647: 278 bp vs. 285 bp haplotypes vs. graphs average Variant 45: 2 haplotypes at x:654: 278 bp vs. 287 bp haplotypes vs. graphs average Variant 46: 2 haplotypes at x:668: 310 bp vs. 320 bp haplotypes vs. graphs average Variant 47: 2 haplotypes at x:669: 310 bp vs. 321 bp haplotypes vs. graphs average Variant 48: 2 haplotypes at x:681: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 49: 2 haplotypes at x:688: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 50: 2 haplotypes at x:698: 280 bp vs. 289 bp haplotypes vs. graphs average Variant 51: 2 haplotypes at x:714: 299 bp vs. 307 bp haplotypes vs. graphs average Variant 52: 2 haplotypes at x:757: 287 bp vs. 299 bp haplotypes vs. graphs average Variant 53: 2 haplotypes at x:775: 273 bp vs. 285 bp haplotypes vs. graphs average Variant 54: 2 haplotypes at x:777: 273 bp vs. 286 bp haplotypes vs. graphs average Variant 55: 2 haplotypes at x:789: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 56: 2 haplotypes at x:795: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 57: 2 haplotypes at x:813: 287 bp vs. 300 bp haplotypes vs. graphs average Variant 58: 2 haplotypes at x:823: 287 bp vs. 302 bp haplotypes vs. graphs average Variant 59: 2 haplotypes at x:827: 319 bp vs. 334 bp haplotypes vs. graphs average Variant 60: 2 haplotypes at x:858: 297 bp vs. 310 bp haplotypes vs. graphs average Variant 61: 2 haplotypes at x:859: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 62: 2 haplotypes at x:860: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 63: 2 haplotypes at x:877: 287 bp vs. 303 bp haplotypes vs. graphs average Variant 64: 2 haplotypes at x:888: 244 bp vs. 262 bp haplotypes vs. graphs average Variant 65: 2 haplotypes at x:899: 243 bp vs. 263 bp haplotypes vs. graphs average Variant 66: 2 haplotypes at x:901: 243 bp vs. 264 bp haplotypes vs. graphs average Variant 67: 2 haplotypes at x:916: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 68: 2 haplotypes at x:917: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 69: 2 haplotypes at x:923: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 70: 2 haplotypes at x:925: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 71: 2 haplotypes at x:929: 222 bp vs. 242 bp haplotypes vs. graphs average Variant 72: 2 haplotypes at x:939: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BlcQBO/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_qCkZMu/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5NlPPg/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..12 ok 1 - vg add can create a graph ok 2 - vg add can create a graph with contig renames ok 3 - vg add produces the same graph from VCFs with different contig names ok 4 - vg add can create a graph from a PackedGraph ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology ok 7 - adding variants adds only the alt bases near large N gaps ok 8 - vg add can create a slightly larger graph ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 3/12 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ijpzg4/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "snarls.xg" Restricting to x from 1 to end Restricting to y from 1 to end t/32_vg_snarls.t ...... 1..9 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 4 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 5 - vcf traversals are the same as exhaustive traversals for tiny graph ok 6 - vcf traversals are the same as exhaustive traversals for inversion ok 7 - vcf traversals are the same as exhaustive traversals for ins_and_del graph ok 8 - correct number of snarls when parallelizing on compoents ok 9 - same number of snarls when parallelizing on components Failed 4/9 subtests [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.matchpaired.fq using 12 threads [vg mpmap] elapsed time 1.0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.matchpaired.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 read pairs. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 1.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 1.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 1.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 1.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 1.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 1.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 1 threads [vg mpmap] elapsed time 1.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 10 -D 50 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 100000 -D 5 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 1.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 12 threads [vg mpmap] elapsed time 1.0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 12 threads warning:[vg mpmap] Could not find 1000 (-b) unambiguous read pair mappings to estimate fragment length ditribution. This can happen due to data issues (e.g. unpaired reads being mapped as pairs) or because the sample size is too large for the read set. Mapping read pairs as independent single-ended reads. [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from input.gam using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0.0 s: Loading graph from t.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from t.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 3 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 0.0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 0.0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 0.0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0.0 s: Mapping finished. Mapped 1 read pairs. t/33_vg_mpmap.t ....... 1..17 ok 1 - MAPQ is 50% without haplotype info ok 2 - haplotype match can disambiguate ok 3 - MAPQ is 50% when paired without haplotype info ok 4 - haplotype match can disambiguate paired ok 5 - use of haplotype-aware mapping is recorded ok 6 - Haplotype-oblivious mapping places read on the wrong contig ok 7 - Haplotype-oblivious mapping places read with MAPQ of 50% ok 8 - Haplotype-aware mapping places read on the right contig ok 9 - Haplotype-aware mapping places read with MAPQ > 50% ok 10 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 11 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 12 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart ok 13 - small batches are still all paired in the output ok 14 - multipath mapping works in scenarios that trigger branch point trimming ok 15 - spliced alignments can be found when aligning RNA ok 16 - paired mapping can identify a splice junction on read 1 ok 17 - paired mapping can identify a splice junction on read 2 ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1TamhC/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mAdC5x/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_q8r9RS/stacktrace.txt Please include the stack trace file in your bug report! t/34_vg_pack.t ........ 1..18 ok 1 - allele observation packing detects 2 SNPs ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - average node qualities are correct # got: '0-0-0-0-0-0-0-0-0-0-' # expected: '20-15-10-10-0-0-0-0-60-60-' Failed 1/18 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_B7Ympc/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "circular_path.xg" t/36_vg_annotate.t .... 1..9 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature ok 7 - annotating with earliest path position produces one position ok 8 - annotating with multiple path positions produces multiple positions not ok 9 - annotations derived from BED can span the end/start joins of circular paths # got: '' # expected: '{"node_id":"1","offset":"5"} # {"node_id":"1"}' Failed 1/9 subtests t/37_vg_gbwt.t ........ 1..91 ok 1 - chromosome X GBWT with vg gbwt ok 2 - chromosome X GBWT with vg index ok 3 - identical construction results with vg gbwt and vg index ok 4 - chromosome X VCF parse ok 5 - chromosome X GBWT from VCF parse ok 6 - identical construction results with vg gbwt and from VCF parse ok 7 - chromosome X: 2 threads ok 8 - chromosome X: 1 contig ok 9 - chromosome X: 2 haplotypes ok 10 - chromosome X: 1 sample ok 11 - chromosome X: 2 thread names ok 12 - chromosome X: 1 contig name ok 13 - chromosome X: 1 sample name ok 14 - chromosome X reference GBWT with vg gbwt ok 15 - chromosome X reference GBWT with vg index ok 16 - identical construction results with vg gbwt and vg index ok 17 - chromosome X reference: 1 thread ok 18 - chromosome X GAF with vg gbwt ok 19 - chromosome X GAF with vg index ok 20 - identical construction results with vg gbwt and vg index ok 21 - chromosome X GAM with vg gbwt ok 22 - identical construction results from GAF and GAM ok 23 - chromosome X subgraph GBWT with vg gbwt ok 24 - no warnings about missing variants ok 25 - chromosome X subgraph GBWT with vg index ok 26 - identical construction results with vg gbwt and vg index ok 27 - insertion merging with multiple chromosomes ok 28 - fast merging with multiple chromosomes ok 29 - identical merging results with the insertion and fast algorithms ok 30 - parallel merging with multiple chromosomes ok 31 - identical merging results with the insertion and parallel algorithms ok 32 - direct construction with multiple chromosomes and a single VCF ok 33 - identical results with direct construction and merging ok 34 - direct construction with multiple chromosomes and multiple VCFs ok 35 - identical construction results with a single VCF and multiple VCFs ok 36 - construction preset: 1000gp ok 37 - multiple chromosomes: 4 threads ok 38 - multiple chromosomes: 2 contigs ok 39 - multiple chromosomes: 2 haplotypes ok 40 - multiple chromosomes: 1 sample ok 41 - paths as contigs with vg gbwt ok 42 - paths as contigs with vg index ok 43 - identical construction results with vg gbwt and vg index ok 44 - paths as contigs: 2 threads ok 45 - paths as contigs: 2 contigs ok 46 - paths as contigs: 1 haplotype ok 47 - paths as contigs: 1 sample ok 48 - paths as samples with vg gbwt ok 49 - paths as samples with vg index ok 50 - paths as samples: 2 threads ok 51 - paths as samples: 1 contig ok 52 - paths as samples: 2 haplotypes ok 53 - paths as samples: 2 samples ok 54 - r-index construction ok 55 - normal merging: non-empty + empty ok 56 - the index remains unchanged ok 57 - normal merging: empty + non-empty ok 58 - the index remains unchanged ok 59 - fast merging: non-empty + empty ok 60 - the index remains unchanged ok 61 - fast merging: empty + non-empty ok 62 - the index remains unchanged ok 63 - parallel merging: non-empty + empty ok 64 - the index remains unchanged ok 65 - parallel merging: empty + non-empty ok 66 - the index remains unchanged ok 67 - haplotypes and paths: 6 threads ok 68 - samples can be removed from a GBWT index ok 69 - haplotypes only: 4 threads ok 70 - threads can be extracted from GBWT ok 71 - correct size for the thread file ok 72 - GBWTGraph construction was successful ok 73 - GBWTGraph was correctly serialized ok 74 - Path cover GBWTGraph construction was successful ok 75 - GBWTGraph was correctly serialized ok 76 - path cover: 32 threads ok 77 - path cover: 2 contigs ok 78 - path cover: 16 haplotypes ok 79 - path cover: 16 samples ok 80 - Local haplotypes GBWTGraph construction was successful ok 81 - GBWTGraph was correctly serialized ok 82 - local haplotypes: 32 threads ok 83 - local haplotypes: 2 contigs ok 84 - local haplotypes: 16 haplotypes ok 85 - local haplotypes: 16 samples ok 86 - Augmented GBWTGraph construction was successful ok 87 - GBWTGraph was correctly serialized ok 88 - augmented: 18 threads ok 89 - augmented: 2 contigs ok 90 - augmented: 2 haplotypes ok 91 - augmented: 17 samples ok t/38_vg_prune.t ....... 1..18 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - empty mapping starts from the right node id ok 17 - the first unfolded graph adds the correct number of nodes to the mapping ok 18 - the second unfolded graph adds the correct number of nodes to the mapping ok t/39_vg_inject.t ...... 1..10 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 1000 reads correct 1 reads correct 0 reads correct 1 reads correct t/40_vg_gamcompare.t .. 1..5 ok 1 - gamcompare completes ok 2 - gamcompare says the truth is correctly mapped ok 3 - Reads annotated with leftmost position only are close enough at a long distance ok 4 - Reads annotated with leftmost position only are too far apart at a short distance ok 5 - Reads annotated with multiple positions only are close enough at a short distance ok t/41_vg_viz.t ......... 1..1 ok 1 - vg viz runs ok t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok t/43_vg_simplify.t .... 1..5 ok 1 - vg simplify runs through when popping small bubbles ok 2 - simplification pops all the bubbles in a simple graph ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants ok 5 - simplification keeps only some variants ok t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/45_vg_sort.t ........ 1..5 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing ok 3 - a vg graph can be sorted topologically ok 4 - a vg graph can be sorted with Eades algorithm without crashing ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing ok warning: [vg index] providing input XG with option -x is deprecated t/46_vg_minimizer.t ... 1..14 ok 1 - default parameters ok 2 - single-threaded construction ok 3 - construction is deterministic ok 4 - syncmer index ok 5 - construction is deterministic ok 6 - minimizer parameters ok 7 - setting -k -w works correctly ok 8 - construction from GBWTGraph ok 9 - construction is deterministic ok 10 - construction with payload ok 11 - construction is deterministic ok 12 - multiple graphs: first ok 13 - multiple graphs: second ok 14 - construction is deterministic ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. t/47_vg_dotplot.t ..... 1..1 ok 1 - vg dotplot runs successfully ok warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DYlmH8/stacktrace.txt Please include the stack trace file in your bug report! warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_MPXmvk/stacktrace.txt Please include the stack trace file in your bug report! warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_qm95OA/stacktrace.txt Please include the stack trace file in your bug report! t/48_vg_convert.t ..... 1..26 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout ODGI conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - odgi conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 14 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 15 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 17 - vg convert gam -> gaf -> gam preserves sequence ok 18 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 19 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 20 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads not ok 21 - split alignment converted using deletions to represent internal offsets # got: '' # expected: 'cs:Z::13-CCAGTGCTC-GCATC:2' ok 22 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 23 - convert gam->gaf->gam on softclipped read preserves sequence ok 24 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 25 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment Failed 1/26 subtests t/49_vg_depth.t ....... 1..4 ok 1 - vg depth gets correct depth from gam ok 2 - vg depth gets correct depth from pack ok 3 - vg depth gets correct number of bins ok 4 - vg depth gets correct depth from gaf ok index file x.fa.fai not found, generating... terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_N7SHeh/stacktrace.txt Please include the stack trace file in your bug report! warning[vg::giraffe]: Finalizing fragment length distribution before reaching maximum sample size mapped 0 reads single ended with 0 pairs of reads left unmapped mean: 0, stdev: 1 terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HPLTqo/stacktrace.txt Please include the stack trace file in your bug report! index file xy.fa.fai not found, generating... t/50_vg_giraffe.t ..... 1..20 ok 1 - a read can be mapped with all indexes specified without crashing ok 2 - a read can be mapped with syncmer indexes without crashing ok 3 - a read can be mapped with just FASTA and VCF without crashing ok 4 - mapping with just a FASTA and a VCF produced JSON-able alignments ok 5 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 6 - mapping with syncmers produces the same alignment as mapping with minimizers ok 7 - unpaired reads lack cross-references ok 8 - paired reads have cross-references not ok 9 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 10 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 11 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 12 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 13 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 14 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 15 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 16 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 17 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 18 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 19 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order ok 20 - surjecting with a sequence dictionary in sorted order produces headers in sorted order Failed 10/20 subtests Test Summary Report ------------------- t/03_vg_view.t (Wstat: 0 Tests: 19 Failed: 3) Failed tests: 5-6, 11 t/05_vg_find.t (Wstat: 0 Tests: 27 Failed: 2) Failed tests: 21-22 t/07_vg_map.t (Wstat: 0 Tests: 54 Failed: 10) Failed tests: 42-51 t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 1) Failed test: 4 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 2) Failed tests: 13, 16 t/15_vg_surject.t (Wstat: 0 Tests: 33 Failed: 10) Failed tests: 11, 17-18, 20-26 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 7) Failed tests: 1-7 t/21_vg_filter.t (Wstat: 0 Tests: 10 Failed: 1) Failed test: 10 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 3) Failed tests: 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 9 Failed: 4) Failed tests: 1-4 t/34_vg_pack.t (Wstat: 0 Tests: 18 Failed: 1) Failed test: 18 t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 1) Failed test: 9 t/48_vg_convert.t (Wstat: 0 Tests: 26 Failed: 1) Failed test: 21 t/50_vg_giraffe.t (Wstat: 0 Tests: 20 Failed: 10) Failed tests: 9-18 Files=49, Tests=758, 594 wallclock secs ( 0.33 usr 0.08 sys + 288.65 cusr 164.27 csys = 453.33 CPU) Result: FAIL make[1]: *** [debian/rules:88: override_dh_auto_test-arch] Error 1 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/2531716 and its subdirectories